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<a href="Bio-module.html">Package Bio</a> ::
Module ParserSupport
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module ParserSupport</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.ParserSupport-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Code to support writing parsers.
Classes:
AbstractParser Base class for parsers.
AbstractConsumer Base class of all Consumers.
TaggingConsumer Consumer that tags output with its event. For debugging
SGMLStrippingConsumer Consumer that strips SGML tags from output.
EventGenerator Generate Biopython Events from Martel XML output
(note that Martel is now DEPRECATED)
Functions:
safe_readline Read a line from a handle, with check for EOF.
safe_peekline Peek at next line, with check for EOF.
read_and_call Read a line from a handle and pass it to a method.
read_and_call_while Read many lines, as long as a condition is met.
read_and_call_until Read many lines, until a condition is met.
attempt_read_and_call Like read_and_call, but forgiving of errors.
is_blank_line Test whether a line is blank.
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Base class for other parsers.
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Base class for other Consumers.
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A Consumer that tags the data stream with the event and prints it
to a handle.
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A consumer that strips off SGML tags.
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Handler to generate events associated with a Martel parsed file.
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<td><span class="summary-sig"><a href="Bio.ParserSupport-module.html#read_and_call" class="summary-sig-name">read_and_call</a>(<span class="summary-sig-arg">uhandle</span>,
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read_and_call(uhandle, method[, start][, end][, contains][, blank][,
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<td><span class="summary-sig"><a href="Bio.ParserSupport-module.html#read_and_call_while" class="summary-sig-name">read_and_call_while</a>(<span class="summary-sig-arg">uhandle</span>,
<span class="summary-sig-arg">method</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
read_and_call_while(uhandle, method[, start][, end][, contains][,
blank][, has_re]) -> number of lines</td>
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<span class="summary-type">number of lines</span>
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<td><span class="summary-sig"><a href="Bio.ParserSupport-module.html#read_and_call_until" class="summary-sig-name">read_and_call_until</a>(<span class="summary-sig-arg">uhandle</span>,
<span class="summary-sig-arg">method</span>,
<span class="summary-sig-arg">start</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">end</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">contains</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">blank</span>=<span class="summary-sig-default">None</span>)</span><br />
Read a line from uhandle and pass it to the method until some
condition is true.</td>
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<span class="summary-type">boolean</span>
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<td><span class="summary-sig"><a href="Bio.ParserSupport-module.html#attempt_read_and_call" class="summary-sig-name">attempt_read_and_call</a>(<span class="summary-sig-arg">uhandle</span>,
<span class="summary-sig-arg">method</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Similar to read_and_call, but returns a boolean specifying whether
the line has passed the checks.</td>
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<td><span class="summary-sig"><a name="_fails_conditions"></a><span class="summary-sig-name">_fails_conditions</span>(<span class="summary-sig-arg">line</span>,
<span class="summary-sig-arg">start</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">end</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">contains</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">blank</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">has_re</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="summary-type">boolean</span>
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<td><span class="summary-sig"><a href="Bio.ParserSupport-module.html#is_blank_line" class="summary-sig-name">is_blank_line</a>(<span class="summary-sig-arg">line</span>,
<span class="summary-sig-arg">allow_spaces</span>=<span class="summary-sig-default">0</span>)</span><br />
Return whether a line is blank.</td>
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<span class="summary-type">line</span>
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<td><span class="summary-sig"><a href="Bio.ParserSupport-module.html#safe_readline" class="summary-sig-name">safe_readline</a>(<span class="summary-sig-arg">handle</span>)</span><br />
Read a line from an UndoHandle and return it.</td>
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<span class="summary-type">line</span>
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<td><span class="summary-sig"><a href="Bio.ParserSupport-module.html#safe_peekline" class="summary-sig-name">safe_peekline</a>(<span class="summary-sig-arg">handle</span>)</span><br />
Peek at the next line in an UndoHandle and return it.</td>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio'"><code class="variable-quote">'</code><code class="variable-string">Bio</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">read_and_call</span>(<span class="sig-arg">uhandle</span>,
<span class="sig-arg">method</span>,
<span class="sig-arg">**keywds</span>)</span>
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<p>read_and_call(uhandle, method[, start][, end][, contains][, blank][,
has_re])</p>
<p>Read a line from uhandle, check it, and pass it to the method. Raises
a ValueError if the line does not pass the checks.</p>
<p>start, end, contains, blank, and has_re specify optional conditions
that the line must pass. start and end specifies what the line must
begin or end with (not counting EOL characters). contains specifies a
substring that must be found in the line. If blank is a true value, then
the line must be blank. has_re should be a regular expression object
with a pattern that the line must match somewhere.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">read_and_call_while</span>(<span class="sig-arg">uhandle</span>,
<span class="sig-arg">method</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.ParserSupport-pysrc.html#read_and_call_while">source code</a></span>
</td>
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<p>read_and_call_while(uhandle, method[, start][, end][, contains][,
blank][, has_re]) -> number of lines</p>
<p>Read a line from uhandle and pass it to the method as long as some
condition is true. Returns the number of lines that were read.</p>
<p>See the docstring for read_and_call for a description of the
parameters.</p>
<dl class="fields">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">read_and_call_until</span>(<span class="sig-arg">uhandle</span>,
<span class="sig-arg">method</span>,
<span class="sig-arg">start</span>=<span class="sig-default">None</span>,
<span class="sig-arg">end</span>=<span class="sig-default">None</span>,
<span class="sig-arg">contains</span>=<span class="sig-default">None</span>,
<span class="sig-arg">blank</span>=<span class="sig-default">None</span>)</span>
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><span class="codelink"><a href="Bio.ParserSupport-pysrc.html#read_and_call_until">source code</a></span>
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<p>Read a line from uhandle and pass it to the method until some
condition is true. Returns the number of lines that were read.</p>
<p>See the docstring for read_and_call for a description of the
parameters.</p>
<dl class="fields">
<dt>Returns: number of lines</dt>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">attempt_read_and_call</span>(<span class="sig-arg">uhandle</span>,
<span class="sig-arg">method</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.ParserSupport-pysrc.html#attempt_read_and_call">source code</a></span>
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<p>Similar to read_and_call, but returns a boolean specifying whether the
line has passed the checks. Does not raise exceptions.</p>
<p>See docs for read_and_call for a description of the function
arguments.</p>
<dl class="fields">
<dt>Returns: boolean</dt>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">is_blank_line</span>(<span class="sig-arg">line</span>,
<span class="sig-arg">allow_spaces</span>=<span class="sig-default">0</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.ParserSupport-pysrc.html#is_blank_line">source code</a></span>
</td>
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<p>Return whether a line is blank. allow_spaces specifies whether to
allow whitespaces in a blank line. A true value signifies that a line
containing whitespaces as well as end-of-line characters should be
considered blank.</p>
<dl class="fields">
<dt>Returns: boolean</dt>
</dl>
</td></tr></table>
</div>
<a name="safe_readline"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">safe_readline</span>(<span class="sig-arg">handle</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.ParserSupport-pysrc.html#safe_readline">source code</a></span>
</td>
</tr></table>
<p>Read a line from an UndoHandle and return it. If there are no more
lines to read, I will raise a ValueError.</p>
<dl class="fields">
<dt>Returns: line</dt>
</dl>
</td></tr></table>
</div>
<a name="safe_peekline"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">safe_peekline</span>(<span class="sig-arg">handle</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.ParserSupport-pysrc.html#safe_peekline">source code</a></span>
</td>
</tr></table>
<p>Peek at the next line in an UndoHandle and return it. If there are no
more lines to peek, I will raise a ValueError.</p>
<dl class="fields">
<dt>Returns: line</dt>
</dl>
</td></tr></table>
</div>
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