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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Nexus-module.html">Package Nexus</a> ::
Module Nexus
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module Nexus</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html">source code</a></span></p>
<p>Nexus class. Parse the contents of a NEXUS file.</p>
<p>Based upon 'NEXUS: An extensible file format for systematic
information' Maddison, Swofford, Maddison. 1997. Syst. Biol.
46(4):590-621</p>
<!-- ==================== CLASSES ==================== -->
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<span class="summary-type"> </span>
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<a href="Bio.Nexus.Nexus.NexusError-class.html" class="summary-name">NexusError</a>
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<a href="Bio.Nexus.Nexus.CharBuffer-class.html" class="summary-name">CharBuffer</a><br />
Helps reading NEXUS-words and characters from a buffer.
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<a href="Bio.Nexus.Nexus.StepMatrix-class.html" class="summary-name">StepMatrix</a><br />
Calculate a stepmatrix for weighted parsimony.
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<a href="Bio.Nexus.Nexus.Commandline-class.html" class="summary-name">Commandline</a><br />
Represent a commandline as command and options.
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<a href="Bio.Nexus.Nexus.Block-class.html" class="summary-name">Block</a><br />
Represent a NEXUS block with block name and list of commandlines.
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<span class="summary-type"> </span>
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<a href="Bio.Nexus.Nexus.Nexus-class.html" class="summary-name">Nexus</a>
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<!-- ==================== FUNCTIONS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#safename" class="summary-sig-name">safename</a>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">mrbayes</span>=<span class="summary-sig-default">False</span>)</span><br />
Return a taxon identifier according to NEXUS standard.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#safename">source code</a></span>
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<td><span class="summary-sig"><a name="quotestrip"></a><span class="summary-sig-name">quotestrip</span>(<span class="summary-sig-arg">word</span>)</span><br />
Remove quotes and/or double quotes around identifiers.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#quotestrip">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#get_start_end" class="summary-sig-name">get_start_end</a>(<span class="summary-sig-arg">sequence</span>,
<span class="summary-sig-arg">skiplist</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">-</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">?</code><code class="variable-quote">'</code><code class="variable-group">]</code></span>)</span><br />
Return position of first and last character which is not in skiplist.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#get_start_end">source code</a></span>
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<td><span class="summary-sig"><a name="_sort_keys_by_values"></a><span class="summary-sig-name">_sort_keys_by_values</span>(<span class="summary-sig-arg">p</span>)</span><br />
Returns a sorted list of keys of p sorted by values of p.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_sort_keys_by_values">source code</a></span>
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<td><span class="summary-sig"><a name="_make_unique"></a><span class="summary-sig-name">_make_unique</span>(<span class="summary-sig-arg">l</span>)</span><br />
Check that all values in list are unique and return a pruned and
sorted list.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_make_unique">source code</a></span>
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<td><span class="summary-sig"><a name="_unique_label"></a><span class="summary-sig-name">_unique_label</span>(<span class="summary-sig-arg">previous_labels</span>,
<span class="summary-sig-arg">label</span>)</span><br />
Returns a unique name if label is already in previous_labels.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_unique_label">source code</a></span>
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<td><span class="summary-sig"><a name="_seqmatrix2strmatrix"></a><span class="summary-sig-name">_seqmatrix2strmatrix</span>(<span class="summary-sig-arg">matrix</span>)</span><br />
Converts a Seq-object matrix to a plain sequence-string matrix.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_seqmatrix2strmatrix">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_compact4nexus"></a><span class="summary-sig-name">_compact4nexus</span>(<span class="summary-sig-arg">orig_list</span>)</span><br />
Transform [1 2 3 5 6 7 8 12 15 18 20] (baseindex 0, used in the Nexus
class) into '2-4 6-9 13-19\3 21' (baseindex 1, used in programs like
Paup or MrBayes.).</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_compact4nexus">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#combine" class="summary-sig-name">combine</a>(<span class="summary-sig-arg">matrices</span>)</span><br />
Combine matrices in [(name,nexus-instance),...] and return new nexus
instance.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#combine">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#_kill_comments_and_break_lines" class="summary-sig-name" onclick="show_private();">_kill_comments_and_break_lines</a>(<span class="summary-sig-arg">text</span>)</span><br />
Delete []-delimited comments out of a file and break into lines
separated by ';'.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_kill_comments_and_break_lines">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#_adjust_lines" class="summary-sig-name" onclick="show_private();">_adjust_lines</a>(<span class="summary-sig-arg">lines</span>)</span><br />
Adjust linebreaks to match ';', strip leading/trailing whitespace.</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_adjust_lines">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_replace_parenthesized_ambigs"></a><span class="summary-sig-name">_replace_parenthesized_ambigs</span>(<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">rev_ambig_values</span>)</span><br />
Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_replace_parenthesized_ambigs">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_get_command_lines"></a><span class="summary-sig-name">_get_command_lines</span>(<span class="summary-sig-arg">file_contents</span>)</span></td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_get_command_lines">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
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<a name="INTERLEAVE"></a><span class="summary-name">INTERLEAVE</span> = <code title="70">70</code>
</td>
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<span class="summary-type"> </span>
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<a href="Bio.Nexus.Nexus-module.html#SPECIAL_COMMANDS" class="summary-name">SPECIAL_COMMANDS</a> = <code title="['charstatelabels',
'charlabels',
'taxlabels',
'taxset',
'charset',
'charpartition',
'taxpartition',
'matrix',
..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">charstatelabels</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">charlabels</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">taxlabel</code><code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.Nexus.Nexus-module.html#KNOWN_NEXUS_BLOCKS" class="summary-name">KNOWN_NEXUS_BLOCKS</a> = <code title="['trees', 'data', 'characters', 'taxa', 'sets', 'codons']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">trees</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">data</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">characters</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">taxa</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="PUNCTUATION"></a><span class="summary-name">PUNCTUATION</span> = <code title="'()[]{}/\\,;:=*\'"`+-<>'"><code class="variable-quote">'</code><code class="variable-string">()[]{}/\\,;:=*\'"`+-<></code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Nexus.Nexus-module.html#MRBAYESSAFE" class="summary-name">MRBAYESSAFE</a> = <code title="'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_'"><code class="variable-quote">'</code><code class="variable-string">abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTU</code><code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="WHITESPACE"></a><span class="summary-name">WHITESPACE</span> = <code title="''' \t
'''"><code class="variable-quote">'</code><code class="variable-string"> \t\n</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="SPECIALCOMMENTS"></a><span class="summary-name">SPECIALCOMMENTS</span> = <code title="['&']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">&</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="CHARSET"></a><span class="summary-name">CHARSET</span> = <code title="'chars'"><code class="variable-quote">'</code><code class="variable-string">chars</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="TAXSET"></a><span class="summary-name">TAXSET</span> = <code title="'taxa'"><code class="variable-quote">'</code><code class="variable-string">taxa</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="CODONPOSITIONS"></a><span class="summary-name">CODONPOSITIONS</span> = <code title="'codonpositions'"><code class="variable-quote">'</code><code class="variable-string">codonpositions</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Nexus.Nexus-module.html#DEFAULTNEXUS" class="summary-name">DEFAULTNEXUS</a> = <code title="'''#NEXUS
begin data; dimensions ntax=0 nchar=0; format datatype=dna; end; '''"><code class="variable-quote">'</code><code class="variable-string">#NEXUS\nbegin data; dimensions ntax=0 nchar=0;</code><code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.Nexus'"><code class="variable-quote">'</code><code class="variable-string">Bio.Nexus</code><code class="variable-quote">'</code></code>
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</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
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<td align="left"><span class="table-header">Function Details</span></td>
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<a name="safename"></a>
<div>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">safename</span>(<span class="sig-arg">name</span>,
<span class="sig-arg">mrbayes</span>=<span class="sig-default">False</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#safename">source code</a></span>
</td>
</tr></table>
<p>Return a taxon identifier according to NEXUS standard.</p>
<p>Wrap quotes around names with punctuation or whitespace, and double
single quotes.</p>
<p>mrbayes=True: write names without quotes, whitespace or punctuation
for the mrbayes software package.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_start_end"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">get_start_end</span>(<span class="sig-arg">sequence</span>,
<span class="sig-arg">skiplist</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">-</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">?</code><code class="variable-quote">'</code><code class="variable-group">]</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#get_start_end">source code</a></span>
</td>
</tr></table>
<p>Return position of first and last character which is not in
skiplist.</p>
<p>Skiplist defaults to ['-','?']).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="combine"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">combine</span>(<span class="sig-arg">matrices</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#combine">source code</a></span>
</td>
</tr></table>
<p>Combine matrices in [(name,nexus-instance),...] and return new nexus
instance.</p>
<p>combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...]
Character sets, character partitions and taxon sets are prefixed,
readjusted and present in the combined matrix.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_kill_comments_and_break_lines"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_kill_comments_and_break_lines</span>(<span class="sig-arg">text</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_kill_comments_and_break_lines">source code</a></span>
</td>
</tr></table>
<p>Delete []-delimited comments out of a file and break into lines
separated by ';'.</p>
<p>stripped_text=_kill_comments_and_break_lines(text): Nested and
multiline comments are allowed. [ and ] symbols within single or double
quotes are ignored, newline ends a quote, all symbols with quotes are
treated the same (thus not quoting inside comments like [this character
']' ends a comment]) Special [&...] and [\...] comments remain
untouched, if not inside standard comment. Quotes inside special [&
and [\ are treated as normal characters, but no nesting inside these
special comments allowed (like [& [\ ]]). ';' ist deleted from
end of line.</p>
<p>NOTE: this function is very slow for large files, and obsolete when
using C extension cnexus</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_adjust_lines"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_adjust_lines</span>(<span class="sig-arg">lines</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_adjust_lines">source code</a></span>
</td>
</tr></table>
<p>Adjust linebreaks to match ';', strip leading/trailing whitespace.</p>
<p>list_of_commandlines=_adjust_lines(input_text) Lines are adjusted so
that no linebreaks occur within a commandline (except matrix command
line)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="SPECIAL_COMMANDS"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SPECIAL_COMMANDS</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">charstatelabels</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">charlabels</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">taxlabels</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">taxset</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">charset</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">charpartition</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">taxpartition</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">matrix</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="KNOWN_NEXUS_BLOCKS"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">KNOWN_NEXUS_BLOCKS</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">trees</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">data</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">characters</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">taxa</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">sets</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">codons</code><code class="variable-quote">'</code><code class="variable-group">]</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="MRBAYESSAFE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">MRBAYESSAFE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-quote">'</code><code class="variable-string">abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_</code><code class="variable-quote">'</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DEFAULTNEXUS"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DEFAULTNEXUS</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-quote">'''</code><code class="variable-string">#NEXUS</code>
<code class="variable-string">begin data; dimensions ntax=0 nchar=0; format datatype=dna; end; </code><code class="variable-quote">'''</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
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