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<a href="Bio-module.html">Package Bio</a> ::
Package SeqIO
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<h1 class="epydoc">Source Code for <a href="Bio.SeqIO-module.html">Package Bio.SeqIO</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2006-2010 by Peter Cock. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment">#Nice link:</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># http://www.ebi.ac.uk/help/formats_frame.html</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">"""Sequence input/output as SeqRecord objects.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Bio.SeqIO is also documented at U{http://biopython.org/wiki/SeqIO} and by</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">a whole chapter in our tutorial:</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> - U{http://biopython.org/DIST/docs/tutorial/Tutorial.html}</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> - U{http://biopython.org/DIST/docs/tutorial/Tutorial.pdf} </tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">Input</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">=====</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">The main function is Bio.SeqIO.parse(...) which takes an input file handle</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">(or in recent versions of Biopython alternatively a filename as a string),</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">and format string. This returns an iterator giving SeqRecord objects:</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> >>> for record in SeqIO.parse("Fasta/f002", "fasta"):</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.id, len(record)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> gi|1348912|gb|G26680|G26680 633</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> gi|1348917|gb|G26685|G26685 413</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> gi|1592936|gb|G29385|G29385 471</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">Note that the parse() function will invoke the relevant parser for the</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">format with its default settings. You may want more control, in which case</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">you need to create a format specific sequence iterator directly.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring">Input - Single Records</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring">======================</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">If you expect your file to contain one-and-only-one record, then we provide</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring">the following 'helper' function which will return a single SeqRecord, or</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring">raise an exception if there are no records or more than one record:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> >>> record = SeqIO.read("Fasta/f001", "fasta")</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> >>> print record.id, len(record)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> gi|3318709|pdb|1A91| 79</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring">This style is useful when you expect a single record only (and would</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring">consider multiple records an error). For example, when dealing with GenBank</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring">files for bacterial genomes or chromosomes, there is normally only a single</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">record. Alternatively, use this with a handle when downloading a single</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring">record from the internet.</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring">However, if you just want the first record from a file containing multiple</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring">record, use the iterator's next() method:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> >>> record = SeqIO.parse("Fasta/f002", "fasta").next()</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> >>> print record.id, len(record)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> gi|1348912|gb|G26680|G26680 633</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring">The above code will work as long as the file contains at least one record.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring">Note that if there is more than one record, the remaining records will be</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring">silently ignored.</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring">Input - Multiple Records</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring">========================</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring">For non-interlaced files (e.g. Fasta, GenBank, EMBL) with multiple records</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring">using a sequence iterator can save you a lot of memory (RAM). There is</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring">less benefit for interlaced file formats (e.g. most multiple alignment file</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring">formats). However, an iterator only lets you access the records one by one.</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring">If you want random access to the records by number, turn this into a list:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> >>> records = list(SeqIO.parse("Fasta/f002", "fasta"))</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(records)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> >>> print records[1].id</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> gi|1348917|gb|G26685|G26685</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring">If you want random access to the records by a key such as the record id,</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring">turn the iterator into a dictionary:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> >>> record_dict = SeqIO.to_dict(SeqIO.parse("Fasta/f002", "fasta"))</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(record_dict)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> >>> print len(record_dict["gi|1348917|gb|G26685|G26685"])</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> 413</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring">However, using list() or the to_dict() function will load all the records</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring">into memory at once, and therefore is not possible on very large files.</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring">Instead, for *some* file formats Bio.SeqIO provides an indexing approach</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring">providing dictionary like access to any record. For example,</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> >>> record_dict = SeqIO.index("Fasta/f002", "fasta")</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(record_dict)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> >>> print len(record_dict["gi|1348917|gb|G26685|G26685"])</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> 413</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring">Many but not all of the supported input file formats can be indexed like</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring">this. For example "fasta", "fastq", "qual" and even the binary format "sff"</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring">work, but alignment formats like "phylip", "clustalw" and "nexus" will not.</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring">In most cases you can also use SeqIO.index to get the record from the file</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring">as a raw string (not a SeqRecord). This can be useful for example to extract</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring">a sub-set of records from a file where SeqIO cannot output the file format</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring">(e.g. the plain text SwissProt format, "swiss") or where it is important to</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring">keep the output 100% identical to the input). For example,</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> >>> record_dict = SeqIO.index("Fasta/f002", "fasta")</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(record_dict)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> >>> print record_dict.get_raw("gi|1348917|gb|G26685|G26685").decode()</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> >gi|1348917|gb|G26685|G26685 human STS STS_D11734.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> CGGAGCCAGCGAGCATATGCTGCATGAGGACCTTTCTATCTTACATTATGGCTGGGAATCTTACTCTTTC</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> ATCTGATACCTTGTTCAGATTTCAAAATAGTTGTAGCCTTATCCTGGTTTTACAGATGTGAAACTTTCAA</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> GAGATTTACTGACTTTCCTAGAATAGTTTCTCTACTGGAAACCTGATGCTTTTATAAGCCATTGTGATTA</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> GGATGACTGTTACAGGCTTAGCTTTGTGTGAAANCCAGTCACCTTTCTCCTAGGTAATGAGTAGTGCTGT</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> TCATATTACTNTAAGTTCTATAGCATACTTGCNATCCTTTANCCATGCTTATCATANGTACCATTTGAGG</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> AATTGNTTTGCCCTTTTGGGTTTNTTNTTGGTAAANNNTTCCCGGGTGGGGGNGGTNNNGAAA</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> >>> print record_dict["gi|1348917|gb|G26685|G26685"].format("fasta")</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> >gi|1348917|gb|G26685|G26685 human STS STS_D11734.</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> CGGAGCCAGCGAGCATATGCTGCATGAGGACCTTTCTATCTTACATTATGGCTGGGAATC</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> TTACTCTTTCATCTGATACCTTGTTCAGATTTCAAAATAGTTGTAGCCTTATCCTGGTTT</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> TACAGATGTGAAACTTTCAAGAGATTTACTGACTTTCCTAGAATAGTTTCTCTACTGGAA</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> ACCTGATGCTTTTATAAGCCATTGTGATTAGGATGACTGTTACAGGCTTAGCTTTGTGTG</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> AAANCCAGTCACCTTTCTCCTAGGTAATGAGTAGTGCTGTTCATATTACTNTAAGTTCTA</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> TAGCATACTTGCNATCCTTTANCCATGCTTATCATANGTACCATTTGAGGAATTGNTTTG</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> CCCTTTTGGGTTTNTTNTTGGTAAANNNTTCCCGGGTGGGGGNGGTNNNGAAA</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring">Here the original file and what Biopython would output differ in the line</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring">wrapping. Also note that under Python 3, the get_raw method will return a</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring">bytes string, hence the use of decode to turn it into a (unicode) string.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring">This is uncessary on Python 2.</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring">Input - Alignments</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring">==================</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring">You can read in alignment files as alignment objects using Bio.AlignIO.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring">Alternatively, reading in an alignment file format via Bio.SeqIO will give</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring">you a SeqRecord for each row of each alignment:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> >>> for record in SeqIO.parse("Clustalw/hedgehog.aln", "clustal"):</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.id, len(record)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> gi|167877390|gb|EDS40773.1| 447</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> gi|167234445|ref|NP_001107837. 447</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> gi|74100009|gb|AAZ99217.1| 447</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> gi|13990994|dbj|BAA33523.2| 447</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> gi|56122354|gb|AAV74328.1| 447</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring">Output</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring">======</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring">Use the function Bio.SeqIO.write(...), which takes a complete set of</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring">SeqRecord objects (either as a list, or an iterator), an output file handle</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring">(or in recent versions of Biopython an output filename as a string) and of</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring">course the file format::</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> from Bio import SeqIO</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> records = ...</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"> SeqIO.write(records, "example.faa", "fasta")</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring">Or, using a handle::</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> from Bio import SeqIO</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> records = ...</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> handle = open("example.faa", "w")</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> SeqIO.write(records, handle, "fasta")</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> handle.close()</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring">You are expected to call this function once (with all your records) and if</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring">using a handle, make sure you close it to flush the data to the hard disk.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring">Output - Advanced</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring">=================</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring">The effect of calling write() multiple times on a single file will vary</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring">depending on the file format, and is best avoided unless you have a strong</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring">reason to do so.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring">If you give a filename, then each time you call write() the existing file</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring">will be overwriten. For sequential files formats (e.g. fasta, genbank) each</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring">"record block" holds a single sequence. For these files it would probably</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring">be safe to call write() multiple times by re-using the same handle.</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring">However, trying this for certain alignment formats (e.g. phylip, clustal,</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring">stockholm) would have the effect of concatenating several multiple sequence</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring">alignments together. Such files are created by the PHYLIP suite of programs</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring">for bootstrap analysis, but it is clearer to do this via Bio.AlignIO instead.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring">Conversion</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring">==========</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring">The Bio.SeqIO.convert(...) function allows an easy interface for simple</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-docstring">file format conversions. Additionally, it may use file format specific</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring">optimisations so this should be the fastest way too.</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring">In general however, you can combine the Bio.SeqIO.parse(...) function with</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring">the Bio.SeqIO.write(...) function for sequence file conversion. Using</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring">generator expressions or generator functions provides a memory efficient way</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring">to perform filtering or other extra operations as part of the process.</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring">File Formats</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-docstring">============</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring">When specifying the file format, use lowercase strings. The same format</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring">names are also used in Bio.AlignIO and include the following:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> - abif - Applied Biosystem's sequencing trace format</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> - ace - Reads the contig sequences from an ACE assembly file.</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> - embl - The EMBL flat file format. Uses Bio.GenBank internally.</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"> - fasta - The generic sequence file format where each record starts with</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-docstring"> an identifer line starting with a ">" character, followed by</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> lines of sequence.</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-docstring"> - fastq - A "FASTA like" format used by Sanger which also stores PHRED</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-docstring"> sequence quality values (with an ASCII offset of 33).</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> - fastq-sanger - An alias for "fastq" for consistency with BioPerl and EMBOSS</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> - fastq-solexa - Original Solexa/Illumnia variant of the FASTQ format which</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> encodes Solexa quality scores (not PHRED quality scores) with an</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> ASCII offset of 64.</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-docstring"> - fastq-illumina - Solexa/Illumina 1.3 to 1.7 variant of the FASTQ format</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-docstring"> which encodes PHRED quality scores with an ASCII offset of 64</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> (not 33). Note as of version 1.8 of the CASAVA pipeline Illumina</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> will produce FASTQ files using the standard Sanger encoding.</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> - genbank - The GenBank or GenPept flat file format.</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-docstring"> - gb - An alias for "genbank", for consistency with NCBI Entrez Utilities</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-docstring"> - ig - The IntelliGenetics file format, apparently the same as the</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-docstring"> MASE alignment format.</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"> - imgt - An EMBL like format from IMGT where the feature tables are more</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"> indented to allow for longer feature types.</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> - phd - Output from PHRED, used by PHRAP and CONSED for input.</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> - pir - A "FASTA like" format introduced by the National Biomedical</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> Research Foundation (NBRF) for the Protein Information Resource</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> (PIR) database, now part of UniProt.</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> - seqxml - SeqXML, simple XML format described in Schmitt et al (2011).</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> - sff - Standard Flowgram Format (SFF), typical output from Roche 454.</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> - sff-trim - Standard Flowgram Format (SFF) with given trimming applied.</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> - swiss - Plain text Swiss-Prot aka UniProt format.</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"> - tab - Simple two column tab separated sequence files, where each</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"> line holds a record's identifier and sequence. For example,</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"> this is used as by Aligent's eArray software when saving</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> microarray probes in a minimal tab delimited text file.</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> - qual - A "FASTA like" format holding PHRED quality values from</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> sequencing DNA, but no actual sequences (usually provided</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> in separate FASTA files).</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> - uniprot-xml - The UniProt XML format (replacement for the SwissProt plain</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"> text format which we call "swiss")</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring">Note that while Bio.SeqIO can read all the above file formats, it cannot</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring">write to all of them.</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring">You can also use any file format supported by Bio.AlignIO, such as "nexus",</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring">"phlip" and "stockholm", which gives you access to the individual sequences</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-docstring">making up each alignment as SeqRecords.</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"epytext en"</tt> <tt class="py-comment">#not just plaintext</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment">#TODO</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-comment"># - define policy on reading aligned sequences with gaps in</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-comment"># (e.g. - and . characters) including how the alphabet interacts</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-comment"># - How best to handle unique/non unique record.id when writing.</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-comment"># For most file formats reading such files is fine; The stockholm</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-comment"># parser would fail.</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-comment"># - MSF multiple alignment format, aka GCG, aka PileUp format (*.msf)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-comment"># http://www.bioperl.org/wiki/MSF_multiple_alignment_format </tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-string">FAO BioPython Developers</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-string">========================</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-string">The way I envision this SeqIO system working as that for any sequence file</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-string">format we have an iterator that returns SeqRecord objects.</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-string">This also applies to interlaced fileformats (like clustal - although that</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-string">is now handled via Bio.AlignIO instead) where the file cannot be read record</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-string">by record. You should still return an iterator, even if the implementation</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-string">could just as easily return a list.</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-string">These file format specific sequence iterators may be implemented as:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-string">* Classes which take a handle for __init__ and provide the __iter__ method</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-string">* Functions that take a handle, and return an iterator object</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-string">* Generator functions that take a handle, and yield SeqRecord objects</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-string">It is then trivial to turn this iterator into a list of SeqRecord objects,</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-string">an in memory dictionary, or a multiple sequence alignment object.</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-string">For building the dictionary by default the id propery of each SeqRecord is</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-string">used as the key. You should always populate the id property, and it should</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-string">be unique in most cases. For some file formats the accession number is a good</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-string">choice. If the file itself contains ambiguous identifiers, don't try and</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-string">dis-ambiguate them - return them as is.</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-string">When adding a new file format, please use the same lower case format name</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-string">as BioPerl, or if they have not defined one, try the names used by EMBOSS.</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-string">See also http://biopython.org/wiki/SeqIO_dev</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-string">--Peter</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-1', 'Seq', 'link-1');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-1');">Seq</a></tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-4', 'SeqRecord', 'link-4');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-5', 'SeqRecord', 'link-4');">SeqRecord</a></tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package Bio.Align=Bio.Align-module.html"><a title="Bio.Align" class="py-name" href="#" onclick="return doclink('link-7', 'Align', 'link-7');">Align</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Class Bio.Align.MultipleSeqAlignment=Bio.Align.MultipleSeqAlignment-class.html"><a title="Bio.Align.MultipleSeqAlignment" class="py-name" href="#" onclick="return doclink('link-8', 'MultipleSeqAlignment', 'link-8');">MultipleSeqAlignment</a></tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Align" class="py-name" href="#" onclick="return doclink('link-10', 'Align', 'link-7');">Align</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Module Bio.Align.Generic=Bio.Align.Generic-module.html"><a title="Bio.Align.Generic" class="py-name" href="#" onclick="return doclink('link-11', 'Generic', 'link-11');">Generic</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-12', 'Alignment', 'link-12');">Alignment</a></tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-13', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-14', 'Alphabet', 'link-14');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-15" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-15', 'Alphabet', 'link-14');">Alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name" targets="Class Bio.Alphabet.AlphabetEncoder=Bio.Alphabet.AlphabetEncoder-class.html"><a title="Bio.Alphabet.AlphabetEncoder" class="py-name" href="#" onclick="return doclink('link-16', 'AlphabetEncoder', 'link-16');">AlphabetEncoder</a></tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name" targets="Function Bio.Alphabet._get_base_alphabet()=Bio.Alphabet-module.html#_get_base_alphabet"><a title="Bio.Alphabet._get_base_alphabet" class="py-name" href="#" onclick="return doclink('link-17', '_get_base_alphabet', 'link-17');">_get_base_alphabet</a></tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-18" class="py-name" targets="Module Bio.SeqIO.AbiIO=Bio.SeqIO.AbiIO-module.html"><a title="Bio.SeqIO.AbiIO" class="py-name" href="#" onclick="return doclink('link-18', 'AbiIO', 'link-18');">AbiIO</a></tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-19" class="py-name" targets="Module Bio.SeqIO.AceIO=Bio.SeqIO.AceIO-module.html"><a title="Bio.SeqIO.AceIO" class="py-name" href="#" onclick="return doclink('link-19', 'AceIO', 'link-19');">AceIO</a></tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-20" class="py-name" targets="Module Bio.AlignIO.FastaIO=Bio.AlignIO.FastaIO-module.html,Module Bio.SeqIO.FastaIO=Bio.SeqIO.FastaIO-module.html"><a title="Bio.AlignIO.FastaIO
Bio.SeqIO.FastaIO" class="py-name" href="#" onclick="return doclink('link-20', 'FastaIO', 'link-20');">FastaIO</a></tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-21" class="py-name" targets="Module Bio.SeqIO.IgIO=Bio.SeqIO.IgIO-module.html"><a title="Bio.SeqIO.IgIO" class="py-name" href="#" onclick="return doclink('link-21', 'IgIO', 'link-21');">IgIO</a></tt> <tt class="py-comment">#IntelliGenetics or MASE format</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-22" class="py-name" targets="Module Bio.SeqIO.InsdcIO=Bio.SeqIO.InsdcIO-module.html"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-22', 'InsdcIO', 'link-22');">InsdcIO</a></tt> <tt class="py-comment">#EMBL and GenBank</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-23" class="py-name" targets="Module Bio.SeqIO.PhdIO=Bio.SeqIO.PhdIO-module.html"><a title="Bio.SeqIO.PhdIO" class="py-name" href="#" onclick="return doclink('link-23', 'PhdIO', 'link-23');">PhdIO</a></tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-24" class="py-name" targets="Module Bio.SeqIO.PirIO=Bio.SeqIO.PirIO-module.html"><a title="Bio.SeqIO.PirIO" class="py-name" href="#" onclick="return doclink('link-24', 'PirIO', 'link-24');">PirIO</a></tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-25" class="py-name" targets="Module Bio.SeqIO.SeqXmlIO=Bio.SeqIO.SeqXmlIO-module.html"><a title="Bio.SeqIO.SeqXmlIO" class="py-name" href="#" onclick="return doclink('link-25', 'SeqXmlIO', 'link-25');">SeqXmlIO</a></tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-26" class="py-name" targets="Module Bio.SeqIO.SffIO=Bio.SeqIO.SffIO-module.html"><a title="Bio.SeqIO.SffIO" class="py-name" href="#" onclick="return doclink('link-26', 'SffIO', 'link-26');">SffIO</a></tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-27" class="py-name" targets="Module Bio.SeqIO.SwissIO=Bio.SeqIO.SwissIO-module.html"><a title="Bio.SeqIO.SwissIO" class="py-name" href="#" onclick="return doclink('link-27', 'SwissIO', 'link-27');">SwissIO</a></tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-28" class="py-name" targets="Module Bio.SeqIO.TabIO=Bio.SeqIO.TabIO-module.html"><a title="Bio.SeqIO.TabIO" class="py-name" href="#" onclick="return doclink('link-28', 'TabIO', 'link-28');">TabIO</a></tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-29" class="py-name" targets="Module Bio.SeqIO.QualityIO=Bio.SeqIO.QualityIO-module.html"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-29', 'QualityIO', 'link-29');">QualityIO</a></tt> <tt class="py-comment">#FastQ and qual files</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-30" class="py-name" targets="Module Bio.SeqIO.UniprotIO=Bio.SeqIO.UniprotIO-module.html"><a title="Bio.SeqIO.UniprotIO" class="py-name" href="#" onclick="return doclink('link-30', 'UniprotIO', 'link-30');">UniprotIO</a></tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-comment">#Convention for format names is "mainname-subtype" in lower case.</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"><tt class="py-comment">#Please use the same names as BioPerl or EMBOSS where possible.</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-comment">#Note that this simple system copes with defining</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-comment">#multiple possible iterators for a given format/extension</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-comment">#with the -subtype suffix</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt class="py-comment">#Most alignment file formats will be handled via Bio.AlignIO</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt id="link-31" class="py-name" targets="Variable Bio.AlignIO._FormatToIterator=Bio.AlignIO-module.html#_FormatToIterator,Variable Bio.SeqIO._FormatToIterator=Bio.SeqIO-module.html#_FormatToIterator"><a title="Bio.AlignIO._FormatToIterator
Bio.SeqIO._FormatToIterator" class="py-name" href="#" onclick="return doclink('link-31', '_FormatToIterator', 'link-31');">_FormatToIterator</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"fasta"</tt> <tt class="py-op">:</tt> <tt id="link-32" class="py-name"><a title="Bio.AlignIO.FastaIO
Bio.SeqIO.FastaIO" class="py-name" href="#" onclick="return doclink('link-32', 'FastaIO', 'link-20');">FastaIO</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Function Bio.SeqIO.FastaIO.FastaIterator()=Bio.SeqIO.FastaIO-module.html#FastaIterator"><a title="Bio.SeqIO.FastaIO.FastaIterator" class="py-name" href="#" onclick="return doclink('link-33', 'FastaIterator', 'link-33');">FastaIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-string">"gb"</tt> <tt class="py-op">:</tt> <tt id="link-34" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-34', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Function Bio.SeqIO.InsdcIO.GenBankIterator()=Bio.SeqIO.InsdcIO-module.html#GenBankIterator"><a title="Bio.SeqIO.InsdcIO.GenBankIterator" class="py-name" href="#" onclick="return doclink('link-35', 'GenBankIterator', 'link-35');">GenBankIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-string">"genbank"</tt> <tt class="py-op">:</tt> <tt id="link-36" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-36', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.SeqIO.InsdcIO.GenBankIterator" class="py-name" href="#" onclick="return doclink('link-37', 'GenBankIterator', 'link-35');">GenBankIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-string">"genbank-cds"</tt> <tt class="py-op">:</tt> <tt id="link-38" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-38', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Function Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator()=Bio.SeqIO.InsdcIO-module.html#GenBankCdsFeatureIterator"><a title="Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator" class="py-name" href="#" onclick="return doclink('link-39', 'GenBankCdsFeatureIterator', 'link-39');">GenBankCdsFeatureIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-string">"embl"</tt> <tt class="py-op">:</tt> <tt id="link-40" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-40', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Function Bio.SeqIO.InsdcIO.EmblIterator()=Bio.SeqIO.InsdcIO-module.html#EmblIterator"><a title="Bio.SeqIO.InsdcIO.EmblIterator" class="py-name" href="#" onclick="return doclink('link-41', 'EmblIterator', 'link-41');">EmblIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-string">"embl-cds"</tt> <tt class="py-op">:</tt> <tt id="link-42" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-42', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Function Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator()=Bio.SeqIO.InsdcIO-module.html#EmblCdsFeatureIterator"><a title="Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator" class="py-name" href="#" onclick="return doclink('link-43', 'EmblCdsFeatureIterator', 'link-43');">EmblCdsFeatureIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-string">"imgt"</tt> <tt class="py-op">:</tt> <tt id="link-44" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-44', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Function Bio.SeqIO.InsdcIO.ImgtIterator()=Bio.SeqIO.InsdcIO-module.html#ImgtIterator"><a title="Bio.SeqIO.InsdcIO.ImgtIterator" class="py-name" href="#" onclick="return doclink('link-45', 'ImgtIterator', 'link-45');">ImgtIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-string">"ig"</tt> <tt class="py-op">:</tt> <tt id="link-46" class="py-name"><a title="Bio.SeqIO.IgIO" class="py-name" href="#" onclick="return doclink('link-46', 'IgIO', 'link-21');">IgIO</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Function Bio.SeqIO.IgIO.IgIterator()=Bio.SeqIO.IgIO-module.html#IgIterator"><a title="Bio.SeqIO.IgIO.IgIterator" class="py-name" href="#" onclick="return doclink('link-47', 'IgIterator', 'link-47');">IgIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-string">"swiss"</tt> <tt class="py-op">:</tt> <tt id="link-48" class="py-name"><a title="Bio.SeqIO.SwissIO" class="py-name" href="#" onclick="return doclink('link-48', 'SwissIO', 'link-27');">SwissIO</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Function Bio.SeqIO.SwissIO.SwissIterator()=Bio.SeqIO.SwissIO-module.html#SwissIterator"><a title="Bio.SeqIO.SwissIO.SwissIterator" class="py-name" href="#" onclick="return doclink('link-49', 'SwissIterator', 'link-49');">SwissIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-string">"phd"</tt> <tt class="py-op">:</tt> <tt id="link-50" class="py-name"><a title="Bio.SeqIO.PhdIO" class="py-name" href="#" onclick="return doclink('link-50', 'PhdIO', 'link-23');">PhdIO</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Function Bio.SeqIO.PhdIO.PhdIterator()=Bio.SeqIO.PhdIO-module.html#PhdIterator"><a title="Bio.SeqIO.PhdIO.PhdIterator" class="py-name" href="#" onclick="return doclink('link-51', 'PhdIterator', 'link-51');">PhdIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-string">"ace"</tt> <tt class="py-op">:</tt> <tt id="link-52" class="py-name"><a title="Bio.SeqIO.AceIO" class="py-name" href="#" onclick="return doclink('link-52', 'AceIO', 'link-19');">AceIO</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Function Bio.SeqIO.AceIO.AceIterator()=Bio.SeqIO.AceIO-module.html#AceIterator"><a title="Bio.SeqIO.AceIO.AceIterator" class="py-name" href="#" onclick="return doclink('link-53', 'AceIterator', 'link-53');">AceIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-string">"tab"</tt> <tt class="py-op">:</tt> <tt id="link-54" class="py-name"><a title="Bio.SeqIO.TabIO" class="py-name" href="#" onclick="return doclink('link-54', 'TabIO', 'link-28');">TabIO</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Function Bio.SeqIO.TabIO.TabIterator()=Bio.SeqIO.TabIO-module.html#TabIterator"><a title="Bio.SeqIO.TabIO.TabIterator" class="py-name" href="#" onclick="return doclink('link-55', 'TabIterator', 'link-55');">TabIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-string">"pir"</tt> <tt class="py-op">:</tt> <tt id="link-56" class="py-name"><a title="Bio.SeqIO.PirIO" class="py-name" href="#" onclick="return doclink('link-56', 'PirIO', 'link-24');">PirIO</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Function Bio.SeqIO.PirIO.PirIterator()=Bio.SeqIO.PirIO-module.html#PirIterator"><a title="Bio.SeqIO.PirIO.PirIterator" class="py-name" href="#" onclick="return doclink('link-57', 'PirIterator', 'link-57');">PirIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-string">"fastq"</tt> <tt class="py-op">:</tt> <tt id="link-58" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-58', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Function Bio.SeqIO.QualityIO.FastqPhredIterator()=Bio.SeqIO.QualityIO-module.html#FastqPhredIterator"><a title="Bio.SeqIO.QualityIO.FastqPhredIterator" class="py-name" href="#" onclick="return doclink('link-59', 'FastqPhredIterator', 'link-59');">FastqPhredIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-string">"fastq-sanger"</tt> <tt class="py-op">:</tt> <tt id="link-60" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-60', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.SeqIO.QualityIO.FastqPhredIterator" class="py-name" href="#" onclick="return doclink('link-61', 'FastqPhredIterator', 'link-59');">FastqPhredIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-string">"fastq-solexa"</tt> <tt class="py-op">:</tt> <tt id="link-62" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-62', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Function Bio.SeqIO.QualityIO.FastqSolexaIterator()=Bio.SeqIO.QualityIO-module.html#FastqSolexaIterator"><a title="Bio.SeqIO.QualityIO.FastqSolexaIterator" class="py-name" href="#" onclick="return doclink('link-63', 'FastqSolexaIterator', 'link-63');">FastqSolexaIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-string">"fastq-illumina"</tt> <tt class="py-op">:</tt> <tt id="link-64" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-64', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Function Bio.SeqIO.QualityIO.FastqIlluminaIterator()=Bio.SeqIO.QualityIO-module.html#FastqIlluminaIterator"><a title="Bio.SeqIO.QualityIO.FastqIlluminaIterator" class="py-name" href="#" onclick="return doclink('link-65', 'FastqIlluminaIterator', 'link-65');">FastqIlluminaIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-string">"qual"</tt> <tt class="py-op">:</tt> <tt id="link-66" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-66', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name" targets="Function Bio.SeqIO.QualityIO.QualPhredIterator()=Bio.SeqIO.QualityIO-module.html#QualPhredIterator"><a title="Bio.SeqIO.QualityIO.QualPhredIterator" class="py-name" href="#" onclick="return doclink('link-67', 'QualPhredIterator', 'link-67');">QualPhredIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-string">"sff"</tt><tt class="py-op">:</tt> <tt id="link-68" class="py-name"><a title="Bio.SeqIO.SffIO" class="py-name" href="#" onclick="return doclink('link-68', 'SffIO', 'link-26');">SffIO</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Function Bio.SeqIO.SffIO.SffIterator()=Bio.SeqIO.SffIO-module.html#SffIterator"><a title="Bio.SeqIO.SffIO.SffIterator" class="py-name" href="#" onclick="return doclink('link-69', 'SffIterator', 'link-69');">SffIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-comment">#Not sure about this in the long run:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-string">"sff-trim"</tt><tt class="py-op">:</tt> <tt id="link-70" class="py-name"><a title="Bio.SeqIO.SffIO" class="py-name" href="#" onclick="return doclink('link-70', 'SffIO', 'link-26');">SffIO</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Function Bio.SeqIO.SffIO._SffTrimIterator()=Bio.SeqIO.SffIO-module.html#_SffTrimIterator"><a title="Bio.SeqIO.SffIO._SffTrimIterator" class="py-name" href="#" onclick="return doclink('link-71', '_SffTrimIterator', 'link-71');">_SffTrimIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-string">"uniprot-xml"</tt><tt class="py-op">:</tt> <tt id="link-72" class="py-name"><a title="Bio.SeqIO.UniprotIO" class="py-name" href="#" onclick="return doclink('link-72', 'UniprotIO', 'link-30');">UniprotIO</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Function Bio.SeqIO.UniprotIO.UniprotIterator()=Bio.SeqIO.UniprotIO-module.html#UniprotIterator"><a title="Bio.SeqIO.UniprotIO.UniprotIterator" class="py-name" href="#" onclick="return doclink('link-73', 'UniprotIterator', 'link-73');">UniprotIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-string">"seqxml"</tt> <tt class="py-op">:</tt> <tt id="link-74" class="py-name"><a title="Bio.SeqIO.SeqXmlIO" class="py-name" href="#" onclick="return doclink('link-74', 'SeqXmlIO', 'link-25');">SeqXmlIO</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Class Bio.SeqIO.SeqXmlIO.SeqXmlIterator=Bio.SeqIO.SeqXmlIO.SeqXmlIterator-class.html"><a title="Bio.SeqIO.SeqXmlIO.SeqXmlIterator" class="py-name" href="#" onclick="return doclink('link-75', 'SeqXmlIterator', 'link-75');">SeqXmlIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-string">"abi"</tt><tt class="py-op">:</tt> <tt id="link-76" class="py-name"><a title="Bio.SeqIO.AbiIO" class="py-name" href="#" onclick="return doclink('link-76', 'AbiIO', 'link-18');">AbiIO</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name" targets="Function Bio.SeqIO.AbiIO.AbiIterator()=Bio.SeqIO.AbiIO-module.html#AbiIterator"><a title="Bio.SeqIO.AbiIO.AbiIterator" class="py-name" href="#" onclick="return doclink('link-77', 'AbiIterator', 'link-77');">AbiIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-string">"abi-trim"</tt><tt class="py-op">:</tt> <tt id="link-78" class="py-name"><a title="Bio.SeqIO.AbiIO" class="py-name" href="#" onclick="return doclink('link-78', 'AbiIO', 'link-18');">AbiIO</a></tt><tt class="py-op">.</tt><tt id="link-79" class="py-name" targets="Function Bio.SeqIO.AbiIO._AbiTrimIterator()=Bio.SeqIO.AbiIO-module.html#_AbiTrimIterator"><a title="Bio.SeqIO.AbiIO._AbiTrimIterator" class="py-name" href="#" onclick="return doclink('link-79', '_AbiTrimIterator', 'link-79');">_AbiTrimIterator</a></tt><tt class="py-op">,</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt id="link-80" class="py-name" targets="Variable Bio.AlignIO._FormatToWriter=Bio.AlignIO-module.html#_FormatToWriter,Variable Bio.SeqIO._FormatToWriter=Bio.SeqIO-module.html#_FormatToWriter"><a title="Bio.AlignIO._FormatToWriter
Bio.SeqIO._FormatToWriter" class="py-name" href="#" onclick="return doclink('link-80', '_FormatToWriter', 'link-80');">_FormatToWriter</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"fasta"</tt> <tt class="py-op">:</tt> <tt id="link-81" class="py-name"><a title="Bio.AlignIO.FastaIO
Bio.SeqIO.FastaIO" class="py-name" href="#" onclick="return doclink('link-81', 'FastaIO', 'link-20');">FastaIO</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name" targets="Class Bio.SeqIO.FastaIO.FastaWriter=Bio.SeqIO.FastaIO.FastaWriter-class.html"><a title="Bio.SeqIO.FastaIO.FastaWriter" class="py-name" href="#" onclick="return doclink('link-82', 'FastaWriter', 'link-82');">FastaWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-string">"gb"</tt> <tt class="py-op">:</tt> <tt id="link-83" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-83', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Class Bio.SeqIO.InsdcIO.GenBankWriter=Bio.SeqIO.InsdcIO.GenBankWriter-class.html"><a title="Bio.SeqIO.InsdcIO.GenBankWriter" class="py-name" href="#" onclick="return doclink('link-84', 'GenBankWriter', 'link-84');">GenBankWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-string">"genbank"</tt> <tt class="py-op">:</tt> <tt id="link-85" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-85', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.SeqIO.InsdcIO.GenBankWriter" class="py-name" href="#" onclick="return doclink('link-86', 'GenBankWriter', 'link-84');">GenBankWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-string">"embl"</tt> <tt class="py-op">:</tt> <tt id="link-87" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-87', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-88" class="py-name" targets="Class Bio.SeqIO.InsdcIO.EmblWriter=Bio.SeqIO.InsdcIO.EmblWriter-class.html"><a title="Bio.SeqIO.InsdcIO.EmblWriter" class="py-name" href="#" onclick="return doclink('link-88', 'EmblWriter', 'link-88');">EmblWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-string">"imgt"</tt> <tt class="py-op">:</tt> <tt id="link-89" class="py-name"><a title="Bio.SeqIO.InsdcIO" class="py-name" href="#" onclick="return doclink('link-89', 'InsdcIO', 'link-22');">InsdcIO</a></tt><tt class="py-op">.</tt><tt id="link-90" class="py-name" targets="Class Bio.SeqIO.InsdcIO.ImgtWriter=Bio.SeqIO.InsdcIO.ImgtWriter-class.html"><a title="Bio.SeqIO.InsdcIO.ImgtWriter" class="py-name" href="#" onclick="return doclink('link-90', 'ImgtWriter', 'link-90');">ImgtWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-string">"tab"</tt> <tt class="py-op">:</tt> <tt id="link-91" class="py-name"><a title="Bio.SeqIO.TabIO" class="py-name" href="#" onclick="return doclink('link-91', 'TabIO', 'link-28');">TabIO</a></tt><tt class="py-op">.</tt><tt id="link-92" class="py-name" targets="Class Bio.SeqIO.TabIO.TabWriter=Bio.SeqIO.TabIO.TabWriter-class.html"><a title="Bio.SeqIO.TabIO.TabWriter" class="py-name" href="#" onclick="return doclink('link-92', 'TabWriter', 'link-92');">TabWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-string">"fastq"</tt> <tt class="py-op">:</tt> <tt id="link-93" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-93', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Class Bio.SeqIO.QualityIO.FastqPhredWriter=Bio.SeqIO.QualityIO.FastqPhredWriter-class.html"><a title="Bio.SeqIO.QualityIO.FastqPhredWriter" class="py-name" href="#" onclick="return doclink('link-94', 'FastqPhredWriter', 'link-94');">FastqPhredWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-string">"fastq-sanger"</tt> <tt class="py-op">:</tt> <tt id="link-95" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-95', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.SeqIO.QualityIO.FastqPhredWriter" class="py-name" href="#" onclick="return doclink('link-96', 'FastqPhredWriter', 'link-94');">FastqPhredWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-string">"fastq-solexa"</tt> <tt class="py-op">:</tt> <tt id="link-97" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-97', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-98" class="py-name" targets="Class Bio.SeqIO.QualityIO.FastqSolexaWriter=Bio.SeqIO.QualityIO.FastqSolexaWriter-class.html"><a title="Bio.SeqIO.QualityIO.FastqSolexaWriter" class="py-name" href="#" onclick="return doclink('link-98', 'FastqSolexaWriter', 'link-98');">FastqSolexaWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-string">"fastq-illumina"</tt> <tt class="py-op">:</tt> <tt id="link-99" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-99', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-100" class="py-name" targets="Class Bio.SeqIO.QualityIO.FastqIlluminaWriter=Bio.SeqIO.QualityIO.FastqIlluminaWriter-class.html"><a title="Bio.SeqIO.QualityIO.FastqIlluminaWriter" class="py-name" href="#" onclick="return doclink('link-100', 'FastqIlluminaWriter', 'link-100');">FastqIlluminaWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-string">"phd"</tt> <tt class="py-op">:</tt> <tt id="link-101" class="py-name"><a title="Bio.SeqIO.PhdIO" class="py-name" href="#" onclick="return doclink('link-101', 'PhdIO', 'link-23');">PhdIO</a></tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Class Bio.SeqIO.PhdIO.PhdWriter=Bio.SeqIO.PhdIO.PhdWriter-class.html"><a title="Bio.SeqIO.PhdIO.PhdWriter" class="py-name" href="#" onclick="return doclink('link-102', 'PhdWriter', 'link-102');">PhdWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-string">"qual"</tt> <tt class="py-op">:</tt> <tt id="link-103" class="py-name"><a title="Bio.SeqIO.QualityIO" class="py-name" href="#" onclick="return doclink('link-103', 'QualityIO', 'link-29');">QualityIO</a></tt><tt class="py-op">.</tt><tt id="link-104" class="py-name" targets="Class Bio.SeqIO.QualityIO.QualPhredWriter=Bio.SeqIO.QualityIO.QualPhredWriter-class.html"><a title="Bio.SeqIO.QualityIO.QualPhredWriter" class="py-name" href="#" onclick="return doclink('link-104', 'QualPhredWriter', 'link-104');">QualPhredWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-string">"sff"</tt> <tt class="py-op">:</tt> <tt id="link-105" class="py-name"><a title="Bio.SeqIO.SffIO" class="py-name" href="#" onclick="return doclink('link-105', 'SffIO', 'link-26');">SffIO</a></tt><tt class="py-op">.</tt><tt id="link-106" class="py-name" targets="Class Bio.SeqIO.SffIO.SffWriter=Bio.SeqIO.SffIO.SffWriter-class.html"><a title="Bio.SeqIO.SffIO.SffWriter" class="py-name" href="#" onclick="return doclink('link-106', 'SffWriter', 'link-106');">SffWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-string">"seqxml"</tt> <tt class="py-op">:</tt> <tt id="link-107" class="py-name"><a title="Bio.SeqIO.SeqXmlIO" class="py-name" href="#" onclick="return doclink('link-107', 'SeqXmlIO', 'link-25');">SeqXmlIO</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Class Bio.SeqIO.SeqXmlIO.SeqXmlWriter=Bio.SeqIO.SeqXmlIO.SeqXmlWriter-class.html"><a title="Bio.SeqIO.SeqXmlIO.SeqXmlWriter" class="py-name" href="#" onclick="return doclink('link-108', 'SeqXmlWriter', 'link-108');">SeqXmlWriter</a></tt><tt class="py-op">,</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt id="link-109" class="py-name" targets="Variable Bio.SeqIO._BinaryFormats=Bio.SeqIO-module.html#_BinaryFormats"><a title="Bio.SeqIO._BinaryFormats" class="py-name" href="#" onclick="return doclink('link-109', '_BinaryFormats', 'link-109');">_BinaryFormats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"sff"</tt><tt class="py-op">,</tt> <tt class="py-string">"sff-trim"</tt><tt class="py-op">,</tt> <tt class="py-string">"abi"</tt><tt class="py-op">,</tt> <tt class="py-string">"abi-trim"</tt><tt class="py-op">]</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> </tt>
<a name="write"></a><div id="write-def"><a name="L382"></a><tt class="py-lineno">382</tt> <a class="py-toggle" href="#" id="write-toggle" onclick="return toggle('write');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#write">write</a><tt class="py-op">(</tt><tt class="py-param">sequences</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="write-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="write-expanded"><a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-docstring">"""Write complete set of sequences to a file.</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-docstring"> - sequences - A list (or iterator) of SeqRecord objects, or (if using</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-docstring"> Biopython 1.54 or later) a single SeqRecord.</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"><tt class="py-docstring"> - handle - File handle object to write to, or filename as string</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"><tt class="py-docstring"> (note older versions of Biopython only took a handle).</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"><tt class="py-docstring"> - format - lower case string describing the file format to write.</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-docstring"> You should close the handle after calling this function.</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"> Returns the number of records written (as an integer).</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-110" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-110', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-111" class="py-name" targets="Package Bio.AlignIO=Bio.AlignIO-module.html"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-111', 'AlignIO', 'link-111');">AlignIO</a></tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-comment">#Try and give helpful error messages:</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-112" class="py-name" targets="Method Bio.Align.Generic.Alignment.format()=Bio.Align.Generic.Alignment-class.html#format,Method Bio.Motif._Motif.Motif.format()=Bio.Motif._Motif.Motif-class.html#format,Method Bio.Phylo.BaseTree.Tree.format()=Bio.Phylo.BaseTree.Tree-class.html#format,Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Method Bio.SeqRecord.SeqRecord.format()=Bio.SeqRecord.SeqRecord-class.html#format"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-112', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Need a string for the file format (lower case)"</tt><tt class="py-op">)</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-113" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-113', 'format', 'link-112');">format</a></tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Format required (lower case string)"</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-114" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-114', 'format', 'link-112');">format</a></tt> <tt class="py-op">!=</tt> <tt id="link-115" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-115', 'format', 'link-112');">format</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Method Bio.Seq.Seq.lower()=Bio.Seq.Seq-class.html#lower,Method Bio.Seq.UnknownSeq.lower()=Bio.Seq.UnknownSeq-class.html#lower,Method Bio.SeqRecord.SeqRecord.lower()=Bio.SeqRecord.SeqRecord-class.html#lower"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-116', 'lower', 'link-116');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Format string '%s' should be lower case"</tt> <tt class="py-op">%</tt> <tt id="link-117" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-117', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">sequences</tt><tt class="py-op">,</tt> <tt id="link-118" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-118', 'SeqRecord', 'link-4');">SeqRecord</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-comment">#This raised an exception in order version of Biopython</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">sequences</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">sequences</tt><tt class="py-op">]</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-119" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-119', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-120" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-120', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-121" class="py-name"><a title="Bio.SeqIO._BinaryFormats" class="py-name" href="#" onclick="return doclink('link-121', '_BinaryFormats', 'link-109');">_BinaryFormats</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt id="link-122" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-122', 'handle', 'link-119');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-123', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-string">"wb"</tt><tt class="py-op">)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt id="link-124" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-124', 'handle', 'link-119');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt id="link-125" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-125', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-name">handle_close</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-name">handle_close</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-comment">#Map the file format to a writer class</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-126" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-126', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-127" class="py-name"><a title="Bio.AlignIO._FormatToWriter
Bio.SeqIO._FormatToWriter" class="py-name" href="#" onclick="return doclink('link-127', '_FormatToWriter', 'link-80');">_FormatToWriter</a></tt><tt class="py-op">:</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">writer_class</tt> <tt class="py-op">=</tt> <tt id="link-128" class="py-name"><a title="Bio.AlignIO._FormatToWriter
Bio.SeqIO._FormatToWriter" class="py-name" href="#" onclick="return doclink('link-128', '_FormatToWriter', 'link-80');">_FormatToWriter</a></tt><tt class="py-op">[</tt><tt id="link-129" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-129', 'format', 'link-112');">format</a></tt><tt class="py-op">]</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt id="link-130" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Method Bio.Seq.UnknownSeq.count()=Bio.Seq.UnknownSeq-class.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-130', 'count', 'link-130');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">writer_class</tt><tt class="py-op">(</tt><tt id="link-131" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-131', 'handle', 'link-119');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name" targets="Method Bio.AlignIO.Interfaces.AlignmentWriter.write_file()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#write_file,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_file()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_file,Method Bio.AlignIO.NexusIO.NexusWriter.write_file()=Bio.AlignIO.NexusIO.NexusWriter-class.html#write_file,Method Bio.SeqIO.Interfaces.SequenceWriter.write_file()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#write_file,Method Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_file()=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_file,Method Bio.SeqIO.SffIO.SffWriter.write_file()=Bio.SeqIO.SffIO.SffWriter-class.html#write_file"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.write_file
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_file
Bio.AlignIO.NexusIO.NexusWriter.write_file
Bio.SeqIO.Interfaces.SequenceWriter.write_file
Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_file
Bio.SeqIO.SffIO.SffWriter.write_file" class="py-name" href="#" onclick="return doclink('link-132', 'write_file', 'link-132');">write_file</a></tt><tt class="py-op">(</tt><tt class="py-name">sequences</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-133" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-133', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-134" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-134', 'AlignIO', 'link-111');">AlignIO</a></tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.AlignIO._FormatToWriter
Bio.SeqIO._FormatToWriter" class="py-name" href="#" onclick="return doclink('link-135', '_FormatToWriter', 'link-80');">_FormatToWriter</a></tt><tt class="py-op">:</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-comment">#Try and turn all the records into a single alignment,</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-comment">#and write that using Bio.AlignIO</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">alignment</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="Bio.Align.MultipleSeqAlignment" class="py-name" href="#" onclick="return doclink('link-136', 'MultipleSeqAlignment', 'link-8');">MultipleSeqAlignment</a></tt><tt class="py-op">(</tt><tt class="py-name">sequences</tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">alignment_count</tt> <tt class="py-op">=</tt> <tt id="link-137" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-137', 'AlignIO', 'link-111');">AlignIO</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-138', 'write', 'link-138');">write</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">alignment</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-139" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-139', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-140" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-140', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">alignment_count</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"Internal error - the underlying writer "</tt> \ </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">" should have returned 1, not %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">alignment_count</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-141', 'count', 'link-130');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alignment</tt><tt class="py-op">)</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">alignment_count</tt><tt class="py-op">,</tt> <tt class="py-name">alignment</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-142" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-142', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-143" class="py-name"><a title="Bio.AlignIO._FormatToIterator
Bio.SeqIO._FormatToIterator" class="py-name" href="#" onclick="return doclink('link-143', '_FormatToIterator', 'link-31');">_FormatToIterator</a></tt> <tt class="py-keyword">or</tt> <tt id="link-144" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-144', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-145" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-145', 'AlignIO', 'link-111');">AlignIO</a></tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.AlignIO._FormatToIterator
Bio.SeqIO._FormatToIterator" class="py-name" href="#" onclick="return doclink('link-146', '_FormatToIterator', 'link-31');">_FormatToIterator</a></tt><tt class="py-op">:</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Reading format '%s' is supported, but not writing"</tt> \ </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt id="link-147" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-147', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown format '%s'"</tt> <tt class="py-op">%</tt> <tt id="link-148" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-148', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-149', 'count', 'link-130');">count</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Internal error - the underlying %s "</tt> \ </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-string">"writer should have returned the record count, not %s"</tt> \ </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-150" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-150', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-151', 'count', 'link-130');">count</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">handle_close</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt id="link-152" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-152', 'handle', 'link-119');">handle</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Method Bio.SeqIO.SffIO._AddTellHandle.close()=Bio.SeqIO.SffIO._AddTellHandle-class.html#close,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.close()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method BioSQL.BioSeqDatabase.DBServer.close()=BioSQL.BioSeqDatabase.DBServer-class.html#close"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-153', 'close', 'link-153');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-154" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-154', 'count', 'link-130');">count</a></tt> </tt>
</div><a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L446"></a><tt class="py-lineno">446</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-docstring">r"""Turns a sequence file into an iterator returning SeqRecords.</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-docstring"> - handle - handle to the file, or the filename as a string</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-docstring"> (note older verions of Biopython only took a handle).</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-docstring"> - format - lower case string describing the file format.</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"> - alphabet - optional Alphabet object, useful when the sequence type</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-docstring"> cannot be automatically inferred from the file itself</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-docstring"> (e.g. format="fasta" or "tab")</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-docstring"> Typical usage, opening a file to read in, and looping over the record(s):</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-docstring"> >>> filename = "Fasta/sweetpea.nu"</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-docstring"> >>> for record in SeqIO.parse(filename, "fasta"):</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"><tt class="py-docstring"> ... print "ID", record.id</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-docstring"> ... print "Sequence length", len(record)</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-docstring"> ... print "Sequence alphabet", record.seq.alphabet</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"><tt class="py-docstring"> ID gi|3176602|gb|U78617.1|LOU78617</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"><tt class="py-docstring"> Sequence length 309</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"><tt class="py-docstring"> Sequence alphabet SingleLetterAlphabet()</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"><tt class="py-docstring"> For file formats like FASTA where the alphabet cannot be determined, it</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"><tt class="py-docstring"> may be useful to specify the alphabet explicitly:</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import generic_dna</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"><tt class="py-docstring"> >>> filename = "Fasta/sweetpea.nu"</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"><tt class="py-docstring"> >>> for record in SeqIO.parse(filename, "fasta", generic_dna):</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"><tt class="py-docstring"> ... print "ID", record.id</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"><tt class="py-docstring"> ... print "Sequence length", len(record)</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"><tt class="py-docstring"> ... print "Sequence alphabet", record.seq.alphabet</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"><tt class="py-docstring"> ID gi|3176602|gb|U78617.1|LOU78617</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"><tt class="py-docstring"> Sequence length 309</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"><tt class="py-docstring"> Sequence alphabet DNAAlphabet()</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"><tt class="py-docstring"> If you have a string 'data' containing the file contents, you must</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"><tt class="py-docstring"> first turn this into a handle in order to parse it:</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"><tt class="py-docstring"> >>> data = ">Alpha\nACCGGATGTA\n>Beta\nAGGCTCGGTTA\n"</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"><tt class="py-docstring"> >>> from StringIO import StringIO</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"><tt class="py-docstring"> >>> for record in SeqIO.parse(StringIO(data), "fasta"):</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.id, record.seq</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt class="py-docstring"> Alpha ACCGGATGTA</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"> Beta AGGCTCGGTTA</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-docstring"> Use the Bio.SeqIO.read(...) function when you expect a single record</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-docstring"> only.</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-comment">#NOTE - The above docstring has some raw \n characters needed</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-comment">#for the StringIO example, hense the whole docstring is in raw</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-comment">#string mode (see the leading r before the opening quote).</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-155" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-155', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-156" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-156', 'AlignIO', 'link-111');">AlignIO</a></tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">handle_close</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-157" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-157', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-comment">#Hack for SFF, will need to make this more general in future</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-158" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-158', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-159" class="py-name"><a title="Bio.SeqIO._BinaryFormats" class="py-name" href="#" onclick="return doclink('link-159', '_BinaryFormats', 'link-109');">_BinaryFormats</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt id="link-160" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-160', 'handle', 'link-119');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt id="link-161" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-161', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt id="link-162" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-162', 'handle', 'link-119');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt id="link-163" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-163', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-string">"rU"</tt><tt class="py-op">)</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-comment">#TODO - On Python 2.5+ use with statement to close handle</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-name">handle_close</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-comment">#Try and give helpful error messages:</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-164" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-164', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Need a string for the file format (lower case)"</tt><tt class="py-op">)</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-165" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-165', 'format', 'link-112');">format</a></tt><tt class="py-op">:</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Format required (lower case string)"</tt><tt class="py-op">)</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-166" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-166', 'format', 'link-112');">format</a></tt> <tt class="py-op">!=</tt> <tt id="link-167" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-167', 'format', 'link-112');">format</a></tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-168', 'lower', 'link-116');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Format string '%s' should be lower case"</tt> <tt class="py-op">%</tt> <tt id="link-169" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-169', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">alphabet</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-170" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-170', 'Alphabet', 'link-14');">Alphabet</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-171" class="py-name"><a title="Bio.Alphabet.AlphabetEncoder" class="py-name" href="#" onclick="return doclink('link-171', 'AlphabetEncoder', 'link-16');">AlphabetEncoder</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid alphabet, %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-comment">#Map the file format to a sequence iterator: </tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-172" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-172', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-173" class="py-name"><a title="Bio.AlignIO._FormatToIterator
Bio.SeqIO._FormatToIterator" class="py-name" href="#" onclick="return doclink('link-173', '_FormatToIterator', 'link-31');">_FormatToIterator</a></tt><tt class="py-op">:</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-name">iterator_generator</tt> <tt class="py-op">=</tt> <tt id="link-174" class="py-name"><a title="Bio.AlignIO._FormatToIterator
Bio.SeqIO._FormatToIterator" class="py-name" href="#" onclick="return doclink('link-174', '_FormatToIterator', 'link-31');">_FormatToIterator</a></tt><tt class="py-op">[</tt><tt id="link-175" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-175', 'format', 'link-112');">format</a></tt><tt class="py-op">]</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">alphabet</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt id="link-176" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-176', 'i', 'link-176');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">iterator_generator</tt><tt class="py-op">(</tt><tt id="link-177" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-177', 'handle', 'link-119');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt id="link-178" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-178', 'i', 'link-176');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">iterator_generator</tt><tt class="py-op">(</tt><tt id="link-179" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-179', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">TypeError</tt><tt class="py-op">:</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt id="link-180" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-180', 'i', 'link-176');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-181" class="py-name" targets="Function Bio.AlignIO._force_alphabet()=Bio.AlignIO-module.html#_force_alphabet,Function Bio.SeqIO._force_alphabet()=Bio.SeqIO-module.html#_force_alphabet"><a title="Bio.AlignIO._force_alphabet
Bio.SeqIO._force_alphabet" class="py-name" href="#" onclick="return doclink('link-181', '_force_alphabet', 'link-181');">_force_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">iterator_generator</tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-182', 'handle', 'link-119');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-183" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-183', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">in</tt> <tt id="link-184" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-184', 'AlignIO', 'link-111');">AlignIO</a></tt><tt class="py-op">.</tt><tt id="link-185" class="py-name"><a title="Bio.AlignIO._FormatToIterator
Bio.SeqIO._FormatToIterator" class="py-name" href="#" onclick="return doclink('link-185', '_FormatToIterator', 'link-31');">_FormatToIterator</a></tt><tt class="py-op">:</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-comment">#Use Bio.AlignIO to read in the alignments</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Can this helper function can be replaced with a generator</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-comment">#expression, or something from itertools?</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt id="link-186" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-186', 'i', 'link-176');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-187" class="py-name" targets="Function Bio.SeqIO._iterate_via_AlignIO()=Bio.SeqIO-module.html#_iterate_via_AlignIO"><a title="Bio.SeqIO._iterate_via_AlignIO" class="py-name" href="#" onclick="return doclink('link-187', '_iterate_via_AlignIO', 'link-187');">_iterate_via_AlignIO</a></tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-188', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-189" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-189', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown format '%s'"</tt> <tt class="py-op">%</tt> <tt id="link-190" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-190', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-comment">#This imposes some overhead... wait until we drop Python 2.4 to fix it</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt id="link-191" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-191', 'i', 'link-176');">i</a></tt><tt class="py-op">:</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">r</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">handle_close</tt><tt class="py-op">:</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt id="link-192" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-192', 'handle', 'link-119');">handle</a></tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-193', 'close', 'link-153');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"><tt class="py-comment">#This is a generator function</tt> </tt>
<a name="_iterate_via_AlignIO"></a><div id="_iterate_via_AlignIO-def"><a name="L547"></a><tt class="py-lineno">547</tt> <a class="py-toggle" href="#" id="_iterate_via_AlignIO-toggle" onclick="return toggle('_iterate_via_AlignIO');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#_iterate_via_AlignIO">_iterate_via_AlignIO</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_iterate_via_AlignIO-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_iterate_via_AlignIO-expanded"><a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over all records in several alignments (PRIVATE)."""</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-194" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-194', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-195" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-195', 'AlignIO', 'link-111');">AlignIO</a></tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-196" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.align()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#align,Class Bio.FSSP.fssp_rec.align=Bio.FSSP.fssp_rec.align-class.html,Function Bio.Wise.align()=Bio.Wise-module.html#align,Function Bio.Wise.dnal.align()=Bio.Wise.dnal-module.html#align,Function Bio.Wise.psw.align()=Bio.Wise.psw-module.html#align,Variable Bio.pairwise2.align=Bio.pairwise2-module.html#align"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-196', 'align', 'link-196');">align</a></tt> <tt class="py-keyword">in</tt> <tt id="link-197" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-197', 'AlignIO', 'link-111');">AlignIO</a></tt><tt class="py-op">.</tt><tt id="link-198" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-198', 'parse', 'link-198');">parse</a></tt><tt class="py-op">(</tt><tt id="link-199" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-199', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-200" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-200', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt id="link-201" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-201', 'align', 'link-196');">align</a></tt><tt class="py-op">:</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> </tt>
<a name="_force_alphabet"></a><div id="_force_alphabet-def"><a name="L554"></a><tt class="py-lineno">554</tt> <a class="py-toggle" href="#" id="_force_alphabet-toggle" onclick="return toggle('_force_alphabet');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#_force_alphabet">_force_alphabet</a><tt class="py-op">(</tt><tt class="py-param">record_iterator</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_force_alphabet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_force_alphabet-expanded"><a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over records, over-riding the alphabet (PRIVATE)."""</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-comment">#Assume the alphabet argument has been pre-validated</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-name">given_base_class</tt> <tt class="py-op">=</tt> <tt id="link-202" class="py-name"><a title="Bio.Alphabet._get_base_alphabet" class="py-name" href="#" onclick="return doclink('link-202', '_get_base_alphabet', 'link-17');">_get_base_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">record_iterator</tt><tt class="py-op">:</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-203" class="py-name"><a title="Bio.Alphabet._get_base_alphabet" class="py-name" href="#" onclick="return doclink('link-203', '_get_base_alphabet', 'link-17');">_get_base_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.seq=Bio.SeqRecord.SeqRecord-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-204', 'seq', 'link-204');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt class="py-name">given_base_class</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-205', 'seq', 'link-204');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">alphabet</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">record</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Specified alphabet %s clashes with "</tt>\ </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-string">"that determined from the file, %s"</tt> \ </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-206', 'seq', 'link-204');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> </tt>
<a name="read"></a><div id="read-def"><a name="L568"></a><tt class="py-lineno">568</tt> <a class="py-toggle" href="#" id="read-toggle" onclick="return toggle('read');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#read">read</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read-expanded"><a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-docstring">"""Turns a sequence file into a single SeqRecord.</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"><tt class="py-docstring"> - handle - handle to the file, or the filename as a string</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"><tt class="py-docstring"> (note older verions of Biopython only took a handle).</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"><tt class="py-docstring"> - format - string describing the file format.</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"><tt class="py-docstring"> - alphabet - optional Alphabet object, useful when the sequence type</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"><tt class="py-docstring"> cannot be automatically inferred from the file itself</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"><tt class="py-docstring"> (e.g. format="fasta" or "tab")</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-docstring"> This function is for use parsing sequence files containing</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"><tt class="py-docstring"> exactly one record. For example, reading a GenBank file:</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"><tt class="py-docstring"> >>> record = SeqIO.read("GenBank/arab1.gb", "genbank")</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"><tt class="py-docstring"> >>> print "ID", record.id</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"><tt class="py-docstring"> ID AC007323.5</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"><tt class="py-docstring"> >>> print "Sequence length", len(record)</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"><tt class="py-docstring"> Sequence length 86436</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"><tt class="py-docstring"> >>> print "Sequence alphabet", record.seq.alphabet</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"><tt class="py-docstring"> Sequence alphabet IUPACAmbiguousDNA()</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"><tt class="py-docstring"> If the handle contains no records, or more than one record,</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"><tt class="py-docstring"> an exception is raised. For example:</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"><tt class="py-docstring"> >>> record = SeqIO.read("GenBank/cor6_6.gb", "genbank")</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"><tt class="py-docstring"> Traceback (most recent call last):</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"><tt class="py-docstring"> ValueError: More than one record found in handle</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"><tt class="py-docstring"> If however you want the first record from a file containing</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"><tt class="py-docstring"> multiple records this function would raise an exception (as</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"><tt class="py-docstring"> shown in the example above). Instead use:</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"><tt class="py-docstring"> >>> record = SeqIO.parse("GenBank/cor6_6.gb", "genbank").next()</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"><tt class="py-docstring"> >>> print "First record's ID", record.id</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"><tt class="py-docstring"> First record's ID X55053.1</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"><tt class="py-docstring"> Use the Bio.SeqIO.parse(handle, format) function if you want</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"><tt class="py-docstring"> to read multiple records from the handle.</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-207" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-207', 'parse', 'link-198');">parse</a></tt><tt class="py-op">(</tt><tt id="link-208" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-208', 'handle', 'link-119');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-209" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-209', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-name">first</tt> <tt class="py-op">=</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.File.UndoHandle.next()=Bio.File.UndoHandle-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.PopGen.GenePop.Controller._FileIterator.next()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-210', 'next', 'link-210');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-name">first</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">first</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"No records found in handle"</tt><tt class="py-op">)</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-name">second</tt> <tt class="py-op">=</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-211" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-211', 'next', 'link-210');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt><tt class="py-op">:</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-name">second</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">second</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"More than one record found in handle"</tt><tt class="py-op">)</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">first</tt> </tt>
</div><a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> </tt>
<a name="to_dict"></a><div id="to_dict-def"><a name="L626"></a><tt class="py-lineno">626</tt> <a class="py-toggle" href="#" id="to_dict-toggle" onclick="return toggle('to_dict');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#to_dict">to_dict</a><tt class="py-op">(</tt><tt class="py-param">sequences</tt><tt class="py-op">,</tt> <tt class="py-param">key_function</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="to_dict-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="to_dict-expanded"><a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt class="py-docstring">"""Turns a sequence iterator or list into a dictionary.</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"><tt class="py-docstring"> - sequences - An iterator that returns SeqRecord objects,</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"><tt class="py-docstring"> or simply a list of SeqRecord objects.</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"><tt class="py-docstring"> - key_function - Optional callback function which when given a</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"><tt class="py-docstring"> SeqRecord should return a unique key for the dictionary.</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"><tt class="py-docstring"> e.g. key_function = lambda rec : rec.name</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"><tt class="py-docstring"> or, key_function = lambda rec : rec.description.split()[0]</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"><tt class="py-docstring"> If key_function is ommitted then record.id is used, on the assumption</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"><tt class="py-docstring"> that the records objects returned are SeqRecords with a unique id.</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"><tt class="py-docstring"> If there are duplicate keys, an error is raised.</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"><tt class="py-docstring"> Example usage, defaulting to using the record.id as key:</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"><tt class="py-docstring"> >>> filename = "GenBank/cor6_6.gb"</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"><tt class="py-docstring"> >>> format = "genbank"</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"><tt class="py-docstring"> >>> id_dict = SeqIO.to_dict(SeqIO.parse(filename, format))</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"><tt class="py-docstring"> >>> print sorted(id_dict)</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"><tt class="py-docstring"> ['AF297471.1', 'AJ237582.1', 'L31939.1', 'M81224.1', 'X55053.1', 'X62281.1']</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"><tt class="py-docstring"> >>> print id_dict["L31939.1"].description</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"><tt class="py-docstring"> Brassica rapa (clone bif72) kin mRNA, complete cds.</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"><tt class="py-docstring"> A more complex example, using the key_function argument in order to</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"><tt class="py-docstring"> use a sequence checksum as the dictionary key:</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.SeqUtils.CheckSum import seguid</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"><tt class="py-docstring"> >>> filename = "GenBank/cor6_6.gb"</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"><tt class="py-docstring"> >>> format = "genbank"</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"><tt class="py-docstring"> >>> seguid_dict = SeqIO.to_dict(SeqIO.parse(filename, format),</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"><tt class="py-docstring"> ... key_function = lambda rec : seguid(rec.seq))</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"><tt class="py-docstring"> >>> for key, record in sorted(seguid_dict.iteritems()):</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"><tt class="py-docstring"> ... print key, record.id</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"><tt class="py-docstring"> /wQvmrl87QWcm9llO4/efg23Vgg AJ237582.1</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"><tt class="py-docstring"> BUg6YxXSKWEcFFH0L08JzaLGhQs L31939.1</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"><tt class="py-docstring"> SabZaA4V2eLE9/2Fm5FnyYy07J4 X55053.1</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"><tt class="py-docstring"> TtWsXo45S3ZclIBy4X/WJc39+CY M81224.1</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"><tt class="py-docstring"> l7gjJFE6W/S1jJn5+1ASrUKW/FA X62281.1</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"><tt class="py-docstring"> uVEYeAQSV5EDQOnFoeMmVea+Oow AF297471.1</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"><tt class="py-docstring"> This approach is not suitable for very large sets of sequences, as all</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"><tt class="py-docstring"> the SeqRecord objects are held in memory. Instead, consider using the</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"><tt class="py-docstring"> Bio.SeqIO.index() function (if it supports your particular file format).</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">key_function</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"> <tt class="py-name">key_function</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">rec</tt> <tt class="py-op">:</tt> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.id()=Bio.Phylo.PhyloXMLIO.Parser-class.html#id,Method Bio.Phylo.PhyloXMLIO.Writer.id()=Bio.Phylo.PhyloXMLIO.Writer-class.html#id"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-212', 'id', 'link-212');">id</a></tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sequences</tt><tt class="py-op">:</tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt class="py-name">key</tt> <tt class="py-op">=</tt> <tt class="py-name">key_function</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">)</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">d</tt><tt class="py-op">:</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Duplicate key '%s'"</tt> <tt class="py-op">%</tt> <tt class="py-name">key</tt><tt class="py-op">)</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-name">d</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">d</tt> </tt>
</div><a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"> </tt>
<a name="index"></a><div id="index-def"><a name="L686"></a><tt class="py-lineno">686</tt> <a class="py-toggle" href="#" id="index-toggle" onclick="return toggle('index');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#index">index</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">key_function</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="index-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="index-expanded"><a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt class="py-docstring">"""Indexes a sequence file and returns a dictionary like object.</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"><tt class="py-docstring"> - filename - string giving name of file to be indexed</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"><tt class="py-docstring"> - format - lower case string describing the file format</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"><tt class="py-docstring"> - alphabet - optional Alphabet object, useful when the sequence type</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"><tt class="py-docstring"> cannot be automatically inferred from the file itself</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"><tt class="py-docstring"> (e.g. format="fasta" or "tab")</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"><tt class="py-docstring"> - key_function - Optional callback function which when given a</tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"><tt class="py-docstring"> SeqRecord identifier string should return a unique</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"><tt class="py-docstring"> key for the dictionary.</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"><tt class="py-docstring"> This indexing function will return a dictionary like object, giving the</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt class="py-docstring"> SeqRecord objects as values:</tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"><tt class="py-docstring"> >>> records = SeqIO.index("Quality/example.fastq", "fastq")</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(records)</tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"><tt class="py-docstring"> >>> sorted(records)</tt> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"><tt class="py-docstring"> ['EAS54_6_R1_2_1_413_324', 'EAS54_6_R1_2_1_443_348', 'EAS54_6_R1_2_1_540_792']</tt> </tt>
<a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"><tt class="py-docstring"> >>> print records["EAS54_6_R1_2_1_540_792"].format("fasta")</tt> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"><tt class="py-docstring"> >EAS54_6_R1_2_1_540_792</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"><tt class="py-docstring"> TTGGCAGGCCAAGGCCGATGGATCA</tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"><tt class="py-docstring"> >>> "EAS54_6_R1_2_1_540_792" in records</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"><tt class="py-docstring"> True</tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"><tt class="py-docstring"> >>> print records.get("Missing", None)</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"><tt class="py-docstring"> None</tt> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"><tt class="py-docstring"> Note that this psuedo dictionary will not support all the methods of a</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"><tt class="py-docstring"> true Python dictionary, for example values() is not defined since this</tt> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"><tt class="py-docstring"> would require loading all of the records into memory at once.</tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"><tt class="py-docstring"> When you call the index function, it will scan through the file, noting</tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"><tt class="py-docstring"> the location of each record. When you access a particular record via the</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"><tt class="py-docstring"> dictionary methods, the code will jump to the appropriate part of the</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"><tt class="py-docstring"> file and then parse that section into a SeqRecord.</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"><tt class="py-docstring"> Note that not all the input formats supported by Bio.SeqIO can be used</tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"><tt class="py-docstring"> with this index function. It is designed to work only with sequential</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"><tt class="py-docstring"> file formats (e.g. "fasta", "gb", "fastq") and is not suitable for any</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"><tt class="py-docstring"> interlaced file format (e.g. alignment formats such as "clustal").</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"><tt class="py-docstring"> For small files, it may be more efficient to use an in memory Python</tt> </tt>
<a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"><tt class="py-docstring"> dictionary, e.g.</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"><tt class="py-docstring"> >>> records = SeqIO.to_dict(SeqIO.parse(open("Quality/example.fastq"), "fastq"))</tt> </tt>
<a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(records)</tt> </tt>
<a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"><tt class="py-docstring"> >>> sorted(records)</tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"><tt class="py-docstring"> ['EAS54_6_R1_2_1_413_324', 'EAS54_6_R1_2_1_443_348', 'EAS54_6_R1_2_1_540_792']</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"><tt class="py-docstring"> >>> print records["EAS54_6_R1_2_1_540_792"].format("fasta")</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"><tt class="py-docstring"> >EAS54_6_R1_2_1_540_792</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"><tt class="py-docstring"> TTGGCAGGCCAAGGCCGATGGATCA</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"><tt class="py-docstring"> As with the to_dict() function, by default the id string of each record</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"><tt class="py-docstring"> is used as the key. You can specify a callback function to transform</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"><tt class="py-docstring"> this (the record identifier string) into your prefered key. For example:</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"><tt class="py-docstring"> >>> def make_tuple(identifier):</tt> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"><tt class="py-docstring"> ... parts = identifier.split("_")</tt> </tt>
<a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"><tt class="py-docstring"> ... return int(parts[-2]), int(parts[-1])</tt> </tt>
<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"><tt class="py-docstring"> >>> records = SeqIO.index("Quality/example.fastq", "fastq",</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"><tt class="py-docstring"> ... key_function=make_tuple)</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(records)</tt> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"><tt class="py-docstring"> >>> sorted(records)</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"><tt class="py-docstring"> [(413, 324), (443, 348), (540, 792)]</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"><tt class="py-docstring"> >>> print records[(540, 792)].format("fasta")</tt> </tt>
<a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"><tt class="py-docstring"> >EAS54_6_R1_2_1_540_792</tt> </tt>
<a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"><tt class="py-docstring"> TTGGCAGGCCAAGGCCGATGGATCA</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"><tt class="py-docstring"> >>> (540, 792) in records</tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"><tt class="py-docstring"> True</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"><tt class="py-docstring"> >>> "EAS54_6_R1_2_1_540_792" in records</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"><tt class="py-docstring"> False</tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"><tt class="py-docstring"> >>> print records.get("Missing", None)</tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"><tt class="py-docstring"> None</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"><tt class="py-docstring"> Another common use case would be indexing an NCBI style FASTA file,</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"><tt class="py-docstring"> where you might want to extract the GI number from the FASTA identifer</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"><tt class="py-docstring"> to use as the dictionary key.</tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"><tt class="py-docstring"> Notice that unlike the to_dict() function, here the key_function does</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"><tt class="py-docstring"> not get given the full SeqRecord to use to generate the key. Doing so</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"><tt class="py-docstring"> would impose a severe performance penalty as it would require the file</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"><tt class="py-docstring"> to be completely parsed while building the index. Right now this is</tt> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"><tt class="py-docstring"> usually avoided.</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"><tt class="py-docstring"> See also: Bio.SeqIO.index_db() and Bio.SeqIO.to_dict()</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-comment">#Try and give helpful error messages:</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Need a filename (not a handle)"</tt><tt class="py-op">)</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-213" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-213', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Need a string for the file format (lower case)"</tt><tt class="py-op">)</tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-214" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-214', 'format', 'link-112');">format</a></tt><tt class="py-op">:</tt> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Format required (lower case string)"</tt><tt class="py-op">)</tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-215" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-215', 'format', 'link-112');">format</a></tt> <tt class="py-op">!=</tt> <tt id="link-216" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-216', 'format', 'link-112');">format</a></tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-217', 'lower', 'link-116');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Format string '%s' should be lower case"</tt> <tt class="py-op">%</tt> <tt id="link-218" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-218', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">alphabet</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-219" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-219', 'Alphabet', 'link-14');">Alphabet</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-220" class="py-name"><a title="Bio.Alphabet.AlphabetEncoder" class="py-name" href="#" onclick="return doclink('link-220', 'AlphabetEncoder', 'link-16');">AlphabetEncoder</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid alphabet, %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt class="py-comment">#Map the file format to a sequence iterator: </tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-221" class="py-name" targets="Module Bio.SeqIO._index=Bio.SeqIO._index-module.html"><a title="Bio.SeqIO._index" class="py-name" href="#" onclick="return doclink('link-221', '_index', 'link-221');">_index</a></tt> <tt class="py-comment">#Lazy import</tt> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-222" class="py-name"><a title="Bio.SeqIO._index" class="py-name" href="#" onclick="return doclink('link-222', '_index', 'link-221');">_index</a></tt><tt class="py-op">.</tt><tt id="link-223" class="py-name" targets="Class Bio.SeqIO._index._IndexedSeqFileDict=Bio.SeqIO._index._IndexedSeqFileDict-class.html"><a title="Bio.SeqIO._index._IndexedSeqFileDict" class="py-name" href="#" onclick="return doclink('link-223', '_IndexedSeqFileDict', 'link-223');">_IndexedSeqFileDict</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt id="link-224" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-224', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">key_function</tt><tt class="py-op">)</tt> </tt>
</div><a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> </tt>
<a name="index_db"></a><div id="index_db-def"><a name="L798"></a><tt class="py-lineno">798</tt> <a class="py-toggle" href="#" id="index_db-toggle" onclick="return toggle('index_db');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#index_db">index_db</a><tt class="py-op">(</tt><tt class="py-param">index_filename</tt><tt class="py-op">,</tt> <tt class="py-param">filenames</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"> <tt class="py-param">key_function</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="index_db-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="index_db-expanded"><a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> <tt class="py-docstring">"""Index several sequence files and return a dictionary like object.</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"><tt class="py-docstring"> The index is stored in an SQLite database rather than in memory (as in the</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"><tt class="py-docstring"> Bio.SeqIO.index(...) function).</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"><tt class="py-docstring"> - index_filename - Where to store the SQLite index</tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"><tt class="py-docstring"> - filenames - list of strings specifying file(s) to be indexed, or when</tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"><tt class="py-docstring"> indexing a single file this can be given as a string.</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"><tt class="py-docstring"> (optional if reloading an existing index, but must match)</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"><tt class="py-docstring"> - format - lower case string describing the file format</tt> </tt>
<a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"><tt class="py-docstring"> (optional if reloading an existing index, but must match)</tt> </tt>
<a name="L811"></a><tt class="py-lineno">811</tt> <tt class="py-line"><tt class="py-docstring"> - alphabet - optional Alphabet object, useful when the sequence type</tt> </tt>
<a name="L812"></a><tt class="py-lineno">812</tt> <tt class="py-line"><tt class="py-docstring"> cannot be automatically inferred from the file itself</tt> </tt>
<a name="L813"></a><tt class="py-lineno">813</tt> <tt class="py-line"><tt class="py-docstring"> (e.g. format="fasta" or "tab")</tt> </tt>
<a name="L814"></a><tt class="py-lineno">814</tt> <tt class="py-line"><tt class="py-docstring"> - key_function - Optional callback function which when given a</tt> </tt>
<a name="L815"></a><tt class="py-lineno">815</tt> <tt class="py-line"><tt class="py-docstring"> SeqRecord identifier string should return a unique</tt> </tt>
<a name="L816"></a><tt class="py-lineno">816</tt> <tt class="py-line"><tt class="py-docstring"> key for the dictionary.</tt> </tt>
<a name="L817"></a><tt class="py-lineno">817</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L818"></a><tt class="py-lineno">818</tt> <tt class="py-line"><tt class="py-docstring"> This indexing function will return a dictionary like object, giving the</tt> </tt>
<a name="L819"></a><tt class="py-lineno">819</tt> <tt class="py-line"><tt class="py-docstring"> SeqRecord objects as values:</tt> </tt>
<a name="L820"></a><tt class="py-lineno">820</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L821"></a><tt class="py-lineno">821</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import generic_protein</tt> </tt>
<a name="L822"></a><tt class="py-lineno">822</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L823"></a><tt class="py-lineno">823</tt> <tt class="py-line"><tt class="py-docstring"> >>> files = ["GenBank/NC_000932.faa", "GenBank/NC_005816.faa"]</tt> </tt>
<a name="L824"></a><tt class="py-lineno">824</tt> <tt class="py-line"><tt class="py-docstring"> >>> def get_gi(name):</tt> </tt>
<a name="L825"></a><tt class="py-lineno">825</tt> <tt class="py-line"><tt class="py-docstring"> ... parts = name.split("|")</tt> </tt>
<a name="L826"></a><tt class="py-lineno">826</tt> <tt class="py-line"><tt class="py-docstring"> ... i = parts.index("gi")</tt> </tt>
<a name="L827"></a><tt class="py-lineno">827</tt> <tt class="py-line"><tt class="py-docstring"> ... assert i != -1</tt> </tt>
<a name="L828"></a><tt class="py-lineno">828</tt> <tt class="py-line"><tt class="py-docstring"> ... return parts[i+1]</tt> </tt>
<a name="L829"></a><tt class="py-lineno">829</tt> <tt class="py-line"><tt class="py-docstring"> >>> idx_name = ":memory:" #use an in memory SQLite DB for this test</tt> </tt>
<a name="L830"></a><tt class="py-lineno">830</tt> <tt class="py-line"><tt class="py-docstring"> >>> records = SeqIO.index_db(idx_name, files, "fasta", generic_protein, get_gi)</tt> </tt>
<a name="L831"></a><tt class="py-lineno">831</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(records)</tt> </tt>
<a name="L832"></a><tt class="py-lineno">832</tt> <tt class="py-line"><tt class="py-docstring"> 95</tt> </tt>
<a name="L833"></a><tt class="py-lineno">833</tt> <tt class="py-line"><tt class="py-docstring"> >>> records["7525076"].description</tt> </tt>
<a name="L834"></a><tt class="py-lineno">834</tt> <tt class="py-line"><tt class="py-docstring"> 'gi|7525076|ref|NP_051101.1| Ycf2 [Arabidopsis thaliana]'</tt> </tt>
<a name="L835"></a><tt class="py-lineno">835</tt> <tt class="py-line"><tt class="py-docstring"> >>> records["45478717"].description</tt> </tt>
<a name="L836"></a><tt class="py-lineno">836</tt> <tt class="py-line"><tt class="py-docstring"> 'gi|45478717|ref|NP_995572.1| pesticin [Yersinia pestis biovar Microtus str. 91001]'</tt> </tt>
<a name="L837"></a><tt class="py-lineno">837</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L838"></a><tt class="py-lineno">838</tt> <tt class="py-line"><tt class="py-docstring"> In this example the two files contain 85 and 10 records respectively.</tt> </tt>
<a name="L839"></a><tt class="py-lineno">839</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L840"></a><tt class="py-lineno">840</tt> <tt class="py-line"><tt class="py-docstring"> See also: Bio.SeqIO.index() and Bio.SeqIO.to_dict()</tt> </tt>
<a name="L841"></a><tt class="py-lineno">841</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L842"></a><tt class="py-lineno">842</tt> <tt class="py-line"> <tt class="py-comment">#Try and give helpful error messages:</tt> </tt>
<a name="L843"></a><tt class="py-lineno">843</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">index_filename</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L844"></a><tt class="py-lineno">844</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Need a string for the index filename"</tt><tt class="py-op">)</tt> </tt>
<a name="L845"></a><tt class="py-lineno">845</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">filenames</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L846"></a><tt class="py-lineno">846</tt> <tt class="py-line"> <tt class="py-comment">#Make the API a little more friendly, and more similar</tt> </tt>
<a name="L847"></a><tt class="py-lineno">847</tt> <tt class="py-line"> <tt class="py-comment">#to Bio.SeqIO.index(...) for indexing just one file.</tt> </tt>
<a name="L848"></a><tt class="py-lineno">848</tt> <tt class="py-line"> <tt class="py-name">filenames</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">filenames</tt><tt class="py-op">]</tt> </tt>
<a name="L849"></a><tt class="py-lineno">849</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">filenames</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">filenames</tt><tt class="py-op">,</tt> <tt id="link-225" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-225', 'list', 'link-225');">list</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L850"></a><tt class="py-lineno">850</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Need a list of filenames (as strings), or one filename"</tt><tt class="py-op">)</tt> </tt>
<a name="L851"></a><tt class="py-lineno">851</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-226" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-226', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-227" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-227', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L852"></a><tt class="py-lineno">852</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Need a string for the file format (lower case)"</tt><tt class="py-op">)</tt> </tt>
<a name="L853"></a><tt class="py-lineno">853</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-228" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-228', 'format', 'link-112');">format</a></tt> <tt class="py-keyword">and</tt> <tt id="link-229" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-229', 'format', 'link-112');">format</a></tt> <tt class="py-op">!=</tt> <tt id="link-230" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-230', 'format', 'link-112');">format</a></tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-231', 'lower', 'link-116');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L854"></a><tt class="py-lineno">854</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Format string '%s' should be lower case"</tt> <tt class="py-op">%</tt> <tt id="link-232" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-232', 'format', 'link-112');">format</a></tt><tt class="py-op">)</tt> </tt>
<a name="L855"></a><tt class="py-lineno">855</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">alphabet</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-233" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-233', 'Alphabet', 'link-14');">Alphabet</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L856"></a><tt class="py-lineno">856</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-234" class="py-name"><a title="Bio.Alphabet.AlphabetEncoder" class="py-name" href="#" onclick="return doclink('link-234', 'AlphabetEncoder', 'link-16');">AlphabetEncoder</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L857"></a><tt class="py-lineno">857</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid alphabet, %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L858"></a><tt class="py-lineno">858</tt> <tt class="py-line"> </tt>
<a name="L859"></a><tt class="py-lineno">859</tt> <tt class="py-line"> <tt class="py-comment">#Map the file format to a sequence iterator: </tt> </tt>
<a name="L860"></a><tt class="py-lineno">860</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-235" class="py-name"><a title="Bio.SeqIO._index" class="py-name" href="#" onclick="return doclink('link-235', '_index', 'link-221');">_index</a></tt> <tt class="py-comment">#Lazy import</tt> </tt>
<a name="L861"></a><tt class="py-lineno">861</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-236" class="py-name"><a title="Bio.SeqIO._index" class="py-name" href="#" onclick="return doclink('link-236', '_index', 'link-221');">_index</a></tt><tt class="py-op">.</tt><tt id="link-237" class="py-name" targets="Class Bio.SeqIO._index._SQLiteManySeqFilesDict=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html"><a title="Bio.SeqIO._index._SQLiteManySeqFilesDict" class="py-name" href="#" onclick="return doclink('link-237', '_SQLiteManySeqFilesDict', 'link-237');">_SQLiteManySeqFilesDict</a></tt><tt class="py-op">(</tt><tt class="py-name">index_filename</tt><tt class="py-op">,</tt> <tt class="py-name">filenames</tt><tt class="py-op">,</tt> <tt id="link-238" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-238', 'format', 'link-112');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L862"></a><tt class="py-lineno">862</tt> <tt class="py-line"> <tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">key_function</tt><tt class="py-op">)</tt> </tt>
</div><a name="L863"></a><tt class="py-lineno">863</tt> <tt class="py-line"> </tt>
<a name="L864"></a><tt class="py-lineno">864</tt> <tt class="py-line"> </tt>
<a name="convert"></a><div id="convert-def"><a name="L865"></a><tt class="py-lineno">865</tt> <a class="py-toggle" href="#" id="convert-toggle" onclick="return toggle('convert');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#convert">convert</a><tt class="py-op">(</tt><tt class="py-param">in_file</tt><tt class="py-op">,</tt> <tt class="py-param">in_format</tt><tt class="py-op">,</tt> <tt class="py-param">out_file</tt><tt class="py-op">,</tt> <tt class="py-param">out_format</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="convert-expanded"><a name="L866"></a><tt class="py-lineno">866</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert between two sequence file formats, return number of records.</tt> </tt>
<a name="L867"></a><tt class="py-lineno">867</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L868"></a><tt class="py-lineno">868</tt> <tt class="py-line"><tt class="py-docstring"> - in_file - an input handle or filename</tt> </tt>
<a name="L869"></a><tt class="py-lineno">869</tt> <tt class="py-line"><tt class="py-docstring"> - in_format - input file format, lower case string</tt> </tt>
<a name="L870"></a><tt class="py-lineno">870</tt> <tt class="py-line"><tt class="py-docstring"> - out_file - an output handle or filename</tt> </tt>
<a name="L871"></a><tt class="py-lineno">871</tt> <tt class="py-line"><tt class="py-docstring"> - out_format - output file format, lower case string</tt> </tt>
<a name="L872"></a><tt class="py-lineno">872</tt> <tt class="py-line"><tt class="py-docstring"> - alphabet - optional alphabet to assume</tt> </tt>
<a name="L873"></a><tt class="py-lineno">873</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L874"></a><tt class="py-lineno">874</tt> <tt class="py-line"><tt class="py-docstring"> NOTE - If you provide an output filename, it will be opened which will</tt> </tt>
<a name="L875"></a><tt class="py-lineno">875</tt> <tt class="py-line"><tt class="py-docstring"> overwrite any existing file without warning. This may happen if even</tt> </tt>
<a name="L876"></a><tt class="py-lineno">876</tt> <tt class="py-line"><tt class="py-docstring"> the conversion is aborted (e.g. an invalid out_format name is given).</tt> </tt>
<a name="L877"></a><tt class="py-lineno">877</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L878"></a><tt class="py-lineno">878</tt> <tt class="py-line"><tt class="py-docstring"> For example, going from a filename to a handle:</tt> </tt>
<a name="L879"></a><tt class="py-lineno">879</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L880"></a><tt class="py-lineno">880</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio import SeqIO</tt> </tt>
<a name="L881"></a><tt class="py-lineno">881</tt> <tt class="py-line"><tt class="py-docstring"> >>> from StringIO import StringIO</tt> </tt>
<a name="L882"></a><tt class="py-lineno">882</tt> <tt class="py-line"><tt class="py-docstring"> >>> handle = StringIO("")</tt> </tt>
<a name="L883"></a><tt class="py-lineno">883</tt> <tt class="py-line"><tt class="py-docstring"> >>> SeqIO.convert("Quality/example.fastq", "fastq", handle, "fasta")</tt> </tt>
<a name="L884"></a><tt class="py-lineno">884</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L885"></a><tt class="py-lineno">885</tt> <tt class="py-line"><tt class="py-docstring"> >>> print handle.getvalue()</tt> </tt>
<a name="L886"></a><tt class="py-lineno">886</tt> <tt class="py-line"><tt class="py-docstring"> >EAS54_6_R1_2_1_413_324</tt> </tt>
<a name="L887"></a><tt class="py-lineno">887</tt> <tt class="py-line"><tt class="py-docstring"> CCCTTCTTGTCTTCAGCGTTTCTCC</tt> </tt>
<a name="L888"></a><tt class="py-lineno">888</tt> <tt class="py-line"><tt class="py-docstring"> >EAS54_6_R1_2_1_540_792</tt> </tt>
<a name="L889"></a><tt class="py-lineno">889</tt> <tt class="py-line"><tt class="py-docstring"> TTGGCAGGCCAAGGCCGATGGATCA</tt> </tt>
<a name="L890"></a><tt class="py-lineno">890</tt> <tt class="py-line"><tt class="py-docstring"> >EAS54_6_R1_2_1_443_348</tt> </tt>
<a name="L891"></a><tt class="py-lineno">891</tt> <tt class="py-line"><tt class="py-docstring"> GTTGCTTCTGGCGTGGGTGGGGGGG</tt> </tt>
<a name="L892"></a><tt class="py-lineno">892</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L893"></a><tt class="py-lineno">893</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L894"></a><tt class="py-lineno">894</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">in_file</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L895"></a><tt class="py-lineno">895</tt> <tt class="py-line"> <tt class="py-comment">#Hack for SFF, will need to make this more general in future</tt> </tt>
<a name="L896"></a><tt class="py-lineno">896</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">in_format</tt> <tt class="py-keyword">in</tt> <tt id="link-239" class="py-name"><a title="Bio.SeqIO._BinaryFormats" class="py-name" href="#" onclick="return doclink('link-239', '_BinaryFormats', 'link-109');">_BinaryFormats</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L897"></a><tt class="py-lineno">897</tt> <tt class="py-line"> <tt class="py-name">in_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">in_file</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L898"></a><tt class="py-lineno">898</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L899"></a><tt class="py-lineno">899</tt> <tt class="py-line"> <tt class="py-name">in_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">in_file</tt><tt class="py-op">,</tt> <tt class="py-string">"rU"</tt><tt class="py-op">)</tt> </tt>
<a name="L900"></a><tt class="py-lineno">900</tt> <tt class="py-line"> <tt class="py-name">in_close</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L901"></a><tt class="py-lineno">901</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L902"></a><tt class="py-lineno">902</tt> <tt class="py-line"> <tt class="py-name">in_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">in_file</tt> </tt>
<a name="L903"></a><tt class="py-lineno">903</tt> <tt class="py-line"> <tt class="py-name">in_close</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L904"></a><tt class="py-lineno">904</tt> <tt class="py-line"> <tt class="py-comment">#Don't open the output file until we've checked the input is OK?</tt> </tt>
<a name="L905"></a><tt class="py-lineno">905</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">out_file</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L906"></a><tt class="py-lineno">906</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">out_format</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"sff"</tt><tt class="py-op">,</tt> <tt class="py-string">"sff_trim"</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L907"></a><tt class="py-lineno">907</tt> <tt class="py-line"> <tt class="py-name">out_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">out_file</tt><tt class="py-op">,</tt> <tt class="py-string">"wb"</tt><tt class="py-op">)</tt> </tt>
<a name="L908"></a><tt class="py-lineno">908</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L909"></a><tt class="py-lineno">909</tt> <tt class="py-line"> <tt class="py-name">out_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">out_file</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L910"></a><tt class="py-lineno">910</tt> <tt class="py-line"> <tt class="py-name">out_close</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L911"></a><tt class="py-lineno">911</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L912"></a><tt class="py-lineno">912</tt> <tt class="py-line"> <tt class="py-name">out_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">out_file</tt> </tt>
<a name="L913"></a><tt class="py-lineno">913</tt> <tt class="py-line"> <tt class="py-name">out_close</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L914"></a><tt class="py-lineno">914</tt> <tt class="py-line"> <tt class="py-comment">#This will check the arguments and issue error messages,</tt> </tt>
<a name="L915"></a><tt class="py-lineno">915</tt> <tt class="py-line"> <tt class="py-comment">#after we have opened the file which is a shame.</tt> </tt>
<a name="L916"></a><tt class="py-lineno">916</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-240" class="py-name" targets="Module Bio.SeqIO._convert=Bio.SeqIO._convert-module.html"><a title="Bio.SeqIO._convert" class="py-name" href="#" onclick="return doclink('link-240', '_convert', 'link-240');">_convert</a></tt> <tt class="py-keyword">import</tt> <tt id="link-241" class="py-name" targets="Function Bio.SeqIO._convert._handle_convert()=Bio.SeqIO._convert-module.html#_handle_convert"><a title="Bio.SeqIO._convert._handle_convert" class="py-name" href="#" onclick="return doclink('link-241', '_handle_convert', 'link-241');">_handle_convert</a></tt> <tt class="py-comment">#Lazy import</tt> </tt>
<a name="L917"></a><tt class="py-lineno">917</tt> <tt class="py-line"> <tt id="link-242" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-242', 'count', 'link-130');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-243" class="py-name"><a title="Bio.SeqIO._convert._handle_convert" class="py-name" href="#" onclick="return doclink('link-243', '_handle_convert', 'link-241');">_handle_convert</a></tt><tt class="py-op">(</tt><tt class="py-name">in_handle</tt><tt class="py-op">,</tt> <tt class="py-name">in_format</tt><tt class="py-op">,</tt> </tt>
<a name="L918"></a><tt class="py-lineno">918</tt> <tt class="py-line"> <tt class="py-name">out_handle</tt><tt class="py-op">,</tt> <tt class="py-name">out_format</tt><tt class="py-op">,</tt> </tt>
<a name="L919"></a><tt class="py-lineno">919</tt> <tt class="py-line"> <tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L920"></a><tt class="py-lineno">920</tt> <tt class="py-line"> <tt class="py-comment">#Must now close any handles we opened</tt> </tt>
<a name="L921"></a><tt class="py-lineno">921</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">in_close</tt><tt class="py-op">:</tt> </tt>
<a name="L922"></a><tt class="py-lineno">922</tt> <tt class="py-line"> <tt class="py-name">in_handle</tt><tt class="py-op">.</tt><tt id="link-244" class="py-name"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-244', 'close', 'link-153');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L923"></a><tt class="py-lineno">923</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">out_close</tt><tt class="py-op">:</tt> </tt>
<a name="L924"></a><tt class="py-lineno">924</tt> <tt class="py-line"> <tt class="py-name">out_handle</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-245', 'close', 'link-153');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L925"></a><tt class="py-lineno">925</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-246" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-246', 'count', 'link-130');">count</a></tt> </tt>
</div><a name="L926"></a><tt class="py-lineno">926</tt> <tt class="py-line"> </tt>
<a name="_test"></a><div id="_test-def"><a name="L927"></a><tt class="py-lineno">927</tt> <a class="py-toggle" href="#" id="_test-toggle" onclick="return toggle('_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO-module.html#_test">_test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_test-expanded"><a name="L928"></a><tt class="py-lineno">928</tt> <tt class="py-line"> <tt class="py-docstring">"""Run the Bio.SeqIO module's doctests.</tt> </tt>
<a name="L929"></a><tt class="py-lineno">929</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L930"></a><tt class="py-lineno">930</tt> <tt class="py-line"><tt class="py-docstring"> This will try and locate the unit tests directory, and run the doctests</tt> </tt>
<a name="L931"></a><tt class="py-lineno">931</tt> <tt class="py-line"><tt class="py-docstring"> from there in order that the relative paths used in the examples work.</tt> </tt>
<a name="L932"></a><tt class="py-lineno">932</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L933"></a><tt class="py-lineno">933</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt> </tt>
<a name="L934"></a><tt class="py-lineno">934</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L935"></a><tt class="py-lineno">935</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">"Tests"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L936"></a><tt class="py-lineno">936</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Runing doctests..."</tt> </tt>
<a name="L937"></a><tt class="py-lineno">937</tt> <tt class="py-line"> <tt class="py-name">cur_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">abspath</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">curdir</tt><tt class="py-op">)</tt> </tt>
<a name="L938"></a><tt class="py-lineno">938</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">".."</tt><tt class="py-op">,</tt> <tt class="py-string">"Tests"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L939"></a><tt class="py-lineno">939</tt> <tt class="py-line"> <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L940"></a><tt class="py-lineno">940</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">cur_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L941"></a><tt class="py-lineno">941</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">cur_dir</tt> </tt>
<a name="L942"></a><tt class="py-lineno">942</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
<a name="L943"></a><tt class="py-lineno">943</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-string">"Tests"</tt><tt class="py-op">,</tt> <tt class="py-string">"Fasta"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L944"></a><tt class="py-lineno">944</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Runing doctests..."</tt> </tt>
<a name="L945"></a><tt class="py-lineno">945</tt> <tt class="py-line"> <tt class="py-name">cur_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">abspath</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">curdir</tt><tt class="py-op">)</tt> </tt>
<a name="L946"></a><tt class="py-lineno">946</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-string">"Tests"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L947"></a><tt class="py-lineno">947</tt> <tt class="py-line"> <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L948"></a><tt class="py-lineno">948</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">cur_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L949"></a><tt class="py-lineno">949</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">cur_dir</tt> </tt>
<a name="L950"></a><tt class="py-lineno">950</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
</div><a name="L951"></a><tt class="py-lineno">951</tt> <tt class="py-line"> </tt>
<a name="L952"></a><tt class="py-lineno">952</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L953"></a><tt class="py-lineno">953</tt> <tt class="py-line"> <tt class="py-comment">#Run the doctests</tt> </tt>
<a name="L954"></a><tt class="py-lineno">954</tt> <tt class="py-line"> <tt id="link-247" class="py-name" targets="Function Bio.Align.Applications._Clustalw._test()=Bio.Align.Applications._Clustalw-module.html#_test,Function Bio.Align.Applications._Dialign._test()=Bio.Align.Applications._Dialign-module.html#_test,Function Bio.Align.Applications._Mafft._test()=Bio.Align.Applications._Mafft-module.html#_test,Function Bio.Align.Applications._Muscle._test()=Bio.Align.Applications._Muscle-module.html#_test,Function Bio.Align.Applications._Prank._test()=Bio.Align.Applications._Prank-module.html#_test,Function Bio.Align.Applications._Probcons._test()=Bio.Align.Applications._Probcons-module.html#_test,Function Bio.Align.Applications._TCoffee._test()=Bio.Align.Applications._TCoffee-module.html#_test,Function Bio.Align.Generic._test()=Bio.Align.Generic-module.html#_test,Function Bio.Align._test()=Bio.Align-module.html#_test,Function Bio.AlignIO.StockholmIO._test()=Bio.AlignIO.StockholmIO-module.html#_test,Function Bio.AlignIO._test()=Bio.AlignIO-module.html#_test,Function Bio.Application._test()=Bio.Application-module.html#_test,Function Bio.Blast.Applications._test()=Bio.Blast.Applications-module.html#_test,Function Bio.DocSQL._test()=Bio.DocSQL-module.html#_test,Function Bio.Emboss.Applications._test()=Bio.Emboss.Applications-module.html#_test,Function Bio.KEGG.Compound._test()=Bio.KEGG.Compound-module.html#_test,Function Bio.KEGG.Enzyme._test()=Bio.KEGG.Enzyme-module.html#_test,Function Bio.Motif._test()=Bio.Motif-module.html#_test,Function Bio.PDB.Selection._test()=Bio.PDB.Selection-module.html#_test,Function Bio.Seq._test()=Bio.Seq-module.html#_test,Function Bio.SeqFeature._test()=Bio.SeqFeature-module.html#_test,Function Bio.SeqIO.AceIO._test()=Bio.SeqIO.AceIO-module.html#_test,Function Bio.SeqIO.PhdIO._test()=Bio.SeqIO.PhdIO-module.html#_test,Function Bio.SeqIO.QualityIO._test()=Bio.SeqIO.QualityIO-module.html#_test,Function Bio.SeqIO._test()=Bio.SeqIO-module.html#_test,Function Bio.SeqRecord._test()=Bio.SeqRecord-module.html#_test,Function Bio.SeqUtils._test()=Bio.SeqUtils-module.html#_test,Function Bio.Sequencing.Applications._Novoalign._test()=Bio.Sequencing.Applications._Novoalign-module.html#_test,Function Bio.Statistics.lowess._test()=Bio.Statistics.lowess-module.html#_test,Function Bio.Wise._test()=Bio.Wise-module.html#_test,Function Bio.Wise.dnal._test()=Bio.Wise.dnal-module.html#_test,Function Bio.Wise.psw._test()=Bio.Wise.psw-module.html#_test"><a title="Bio.Align.Applications._Clustalw._test
Bio.Align.Applications._Dialign._test
Bio.Align.Applications._Mafft._test
Bio.Align.Applications._Muscle._test
Bio.Align.Applications._Prank._test
Bio.Align.Applications._Probcons._test
Bio.Align.Applications._TCoffee._test
Bio.Align.Generic._test
Bio.Align._test
Bio.AlignIO.StockholmIO._test
Bio.AlignIO._test
Bio.Application._test
Bio.Blast.Applications._test
Bio.DocSQL._test
Bio.Emboss.Applications._test
Bio.KEGG.Compound._test
Bio.KEGG.Enzyme._test
Bio.Motif._test
Bio.PDB.Selection._test
Bio.Seq._test
Bio.SeqFeature._test
Bio.SeqIO.AceIO._test
Bio.SeqIO.PhdIO._test
Bio.SeqIO.QualityIO._test
Bio.SeqIO._test
Bio.SeqRecord._test
Bio.SeqUtils._test
Bio.Sequencing.Applications._Novoalign._test
Bio.Statistics.lowess._test
Bio.Wise._test
Bio.Wise.dnal._test
Bio.Wise.psw._test" class="py-name" href="#" onclick="return doclink('link-247', '_test', 'link-247');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L955"></a><tt class="py-lineno">955</tt> <tt class="py-line"> </tt><script type="text/javascript">
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</pre>
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