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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Blast-module.html">Package Blast</a> ::
<a href="Bio.Blast.NCBIXML-module.html">Module NCBIXML</a> ::
Class BlastParser
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BlastParser</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser">source code</a></span></p>
<pre class="base-tree">
xml.sax.handler.ContentHandler --+
|
<a href="Bio.Blast.NCBIXML._XMLparser-class.html" onclick="show_private();">_XMLparser</a> --+
|
<strong class="uidshort">BlastParser</strong>
</pre>
<hr />
<p>Parse XML BLAST data into a Record.Blast object</p>
<p>All XML 'action' methods are private methods and may be: _start_TAG
called when the start tag is found _end_TAG called when the end
tag is found</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">debug</span>=<span class="summary-sig-default">0</span>)</span><br />
Constructor</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="reset"></a><span class="summary-sig-name">reset</span>(<span class="summary-sig-arg">self</span>)</span><br />
Reset all the data allowing reuse of the BlastParser() object</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser.reset">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#parse" class="summary-sig-name">parse</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">handler</span>)</span><br />
Parses the XML data</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser.parse">source code</a></span>
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<td><span class="summary-sig"><a name="_start_Iteration"></a><span class="summary-sig-name">_start_Iteration</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._start_Iteration">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Iteration"></a><span class="summary-sig-name">_end_Iteration</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Iteration">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_program" class="summary-sig-name" onclick="show_private();">_end_BlastOutput_program</a>(<span class="summary-sig-arg">self</span>)</span><br />
BLAST program, e.g., blastp, blastn, etc.</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_program">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_version" class="summary-sig-name" onclick="show_private();">_end_BlastOutput_version</a>(<span class="summary-sig-arg">self</span>)</span><br />
version number and date of the BLAST engine.</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_version">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_reference" class="summary-sig-name" onclick="show_private();">_end_BlastOutput_reference</a>(<span class="summary-sig-arg">self</span>)</span><br />
a reference to the article describing the algorithm</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_reference">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_db" class="summary-sig-name" onclick="show_private();">_end_BlastOutput_db</a>(<span class="summary-sig-arg">self</span>)</span><br />
the database(s) searched</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_db">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_query_ID" class="summary-sig-name" onclick="show_private();">_end_BlastOutput_query_ID</a>(<span class="summary-sig-arg">self</span>)</span><br />
the identifier of the query</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_query_ID">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_query_def" class="summary-sig-name" onclick="show_private();">_end_BlastOutput_query_def</a>(<span class="summary-sig-arg">self</span>)</span><br />
the definition line of the query</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_query_def">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.Blast.NCBIXML.BlastParser-class.html#_end_BlastOutput_query_len" class="summary-sig-name" onclick="show_private();">_end_BlastOutput_query_len</a>(<span class="summary-sig-arg">self</span>)</span><br />
the length of the query</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_query_len">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Iteration_query_ID"></a><span class="summary-sig-name">_end_Iteration_query_ID</span>(<span class="summary-sig-arg">self</span>)</span><br />
the identifier of the query</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Iteration_query_ID">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Iteration_query_def"></a><span class="summary-sig-name">_end_Iteration_query_def</span>(<span class="summary-sig-arg">self</span>)</span><br />
the definition line of the query</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Iteration_query_def">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Iteration_query_len"></a><span class="summary-sig-name">_end_Iteration_query_len</span>(<span class="summary-sig-arg">self</span>)</span><br />
the length of the query</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Iteration_query_len">source code</a></span>
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<td><span class="summary-sig"><a name="_end_BlastOutput_hits"></a><span class="summary-sig-name">_end_BlastOutput_hits</span>(<span class="summary-sig-arg">self</span>)</span><br />
hits to the database sequences, one for every sequence</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_hits">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Parameters_matrix"></a><span class="summary-sig-name">_end_Parameters_matrix</span>(<span class="summary-sig-arg">self</span>)</span><br />
matrix used (-M)</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Parameters_matrix">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Parameters_expect"></a><span class="summary-sig-name">_end_Parameters_expect</span>(<span class="summary-sig-arg">self</span>)</span><br />
expect values cutoff (-e)</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Parameters_expect">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Parameters_sc_match"></a><span class="summary-sig-name">_end_Parameters_sc_match</span>(<span class="summary-sig-arg">self</span>)</span><br />
match score for nucleotide-nucleotide comparaison (-r)</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Parameters_sc_match">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Parameters_sc_mismatch"></a><span class="summary-sig-name">_end_Parameters_sc_mismatch</span>(<span class="summary-sig-arg">self</span>)</span><br />
mismatch penalty for nucleotide-nucleotide comparaison (-r)</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Parameters_sc_mismatch">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Parameters_gap_open"></a><span class="summary-sig-name">_end_Parameters_gap_open</span>(<span class="summary-sig-arg">self</span>)</span><br />
gap existence cost (-G)</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Parameters_gap_open">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Parameters_gap_extend"></a><span class="summary-sig-name">_end_Parameters_gap_extend</span>(<span class="summary-sig-arg">self</span>)</span><br />
gap extension cose (-E)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Parameters_gap_extend">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Parameters_filter"></a><span class="summary-sig-name">_end_Parameters_filter</span>(<span class="summary-sig-arg">self</span>)</span><br />
filtering options (-F)</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Parameters_filter">source code</a></span>
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<td><span class="summary-sig"><a name="_start_Hit"></a><span class="summary-sig-name">_start_Hit</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._start_Hit">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Hit"></a><span class="summary-sig-name">_end_Hit</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hit">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Hit_id"></a><span class="summary-sig-name">_end_Hit_id</span>(<span class="summary-sig-arg">self</span>)</span><br />
identifier of the database sequence</td>
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<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hit_id">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Hit_def"></a><span class="summary-sig-name">_end_Hit_def</span>(<span class="summary-sig-arg">self</span>)</span><br />
definition line of the database sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hit_def">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Hit_accession"></a><span class="summary-sig-name">_end_Hit_accession</span>(<span class="summary-sig-arg">self</span>)</span><br />
accession of the database sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hit_accession">source code</a></span>
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<td><span class="summary-sig"><a name="_end_Hit_len"></a><span class="summary-sig-name">_end_Hit_len</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hit_len">source code</a></span>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_start_Hsp"></a><span class="summary-sig-name">_start_Hsp</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._start_Hsp">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_score"></a><span class="summary-sig-name">_end_Hsp_score</span>(<span class="summary-sig-arg">self</span>)</span><br />
raw score of HSP</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_score">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_bit_score"></a><span class="summary-sig-name">_end_Hsp_bit_score</span>(<span class="summary-sig-arg">self</span>)</span><br />
bit score of HSP</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_bit_score">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_evalue"></a><span class="summary-sig-name">_end_Hsp_evalue</span>(<span class="summary-sig-arg">self</span>)</span><br />
expect value value of the HSP</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_evalue">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_query_from"></a><span class="summary-sig-name">_end_Hsp_query_from</span>(<span class="summary-sig-arg">self</span>)</span><br />
offset of query at the start of the alignment (one-offset)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_query_from">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_query_to"></a><span class="summary-sig-name">_end_Hsp_query_to</span>(<span class="summary-sig-arg">self</span>)</span><br />
offset of query at the end of the alignment (one-offset)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_query_to">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_hit_from"></a><span class="summary-sig-name">_end_Hsp_hit_from</span>(<span class="summary-sig-arg">self</span>)</span><br />
offset of the database at the start of the alignment (one-offset)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_hit_from">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_hit_to"></a><span class="summary-sig-name">_end_Hsp_hit_to</span>(<span class="summary-sig-arg">self</span>)</span><br />
offset of the database at the end of the alignment (one-offset)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_hit_to">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_query_frame"></a><span class="summary-sig-name">_end_Hsp_query_frame</span>(<span class="summary-sig-arg">self</span>)</span><br />
frame of the query if applicable</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_query_frame">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_hit_frame"></a><span class="summary-sig-name">_end_Hsp_hit_frame</span>(<span class="summary-sig-arg">self</span>)</span><br />
frame of the database sequence if applicable</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_hit_frame">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_identity"></a><span class="summary-sig-name">_end_Hsp_identity</span>(<span class="summary-sig-arg">self</span>)</span><br />
number of identities in the alignment</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_identity">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_positive"></a><span class="summary-sig-name">_end_Hsp_positive</span>(<span class="summary-sig-arg">self</span>)</span><br />
number of positive (conservative) substitutions in the alignment</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_positive">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_gaps"></a><span class="summary-sig-name">_end_Hsp_gaps</span>(<span class="summary-sig-arg">self</span>)</span><br />
number of gaps in the alignment</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_gaps">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_align_len"></a><span class="summary-sig-name">_end_Hsp_align_len</span>(<span class="summary-sig-arg">self</span>)</span><br />
length of the alignment</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_align_len">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_qseq"></a><span class="summary-sig-name">_end_Hsp_qseq</span>(<span class="summary-sig-arg">self</span>)</span><br />
alignment string for the query</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_qseq">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_hseq"></a><span class="summary-sig-name">_end_Hsp_hseq</span>(<span class="summary-sig-arg">self</span>)</span><br />
alignment string for the database</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_hseq">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Hsp_midline"></a><span class="summary-sig-name">_end_Hsp_midline</span>(<span class="summary-sig-arg">self</span>)</span><br />
Formatting middle line as normally seen in BLAST report</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Hsp_midline">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Statistics_db_num"></a><span class="summary-sig-name">_end_Statistics_db_num</span>(<span class="summary-sig-arg">self</span>)</span><br />
number of sequences in the database</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Statistics_db_num">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Statistics_db_len"></a><span class="summary-sig-name">_end_Statistics_db_len</span>(<span class="summary-sig-arg">self</span>)</span><br />
number of letters in the database</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Statistics_db_len">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Statistics_hsp_len"></a><span class="summary-sig-name">_end_Statistics_hsp_len</span>(<span class="summary-sig-arg">self</span>)</span><br />
the effective HSP length</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Statistics_hsp_len">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Statistics_eff_space"></a><span class="summary-sig-name">_end_Statistics_eff_space</span>(<span class="summary-sig-arg">self</span>)</span><br />
the effective search space</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Statistics_eff_space">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Statistics_kappa"></a><span class="summary-sig-name">_end_Statistics_kappa</span>(<span class="summary-sig-arg">self</span>)</span><br />
Karlin-Altschul parameter K</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Statistics_kappa">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Statistics_lambda"></a><span class="summary-sig-name">_end_Statistics_lambda</span>(<span class="summary-sig-arg">self</span>)</span><br />
Karlin-Altschul parameter Lambda</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Statistics_lambda">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_end_Statistics_entropy"></a><span class="summary-sig-name">_end_Statistics_entropy</span>(<span class="summary-sig-arg">self</span>)</span><br />
Karlin-Altschul parameter H</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_Statistics_entropy">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Blast.NCBIXML._XMLparser-class.html" onclick="show_private();">_XMLparser</a></code></b>:
<code><a href="Bio.Blast.NCBIXML._XMLparser-class.html#characters">characters</a></code>,
<code><a href="Bio.Blast.NCBIXML._XMLparser-class.html#endElement">endElement</a></code>,
<code><a href="Bio.Blast.NCBIXML._XMLparser-class.html#startElement">startElement</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Blast.NCBIXML._XMLparser-class.html" onclick="show_private();">_XMLparser</a></code></b> (private):
<code><a href="Bio.Blast.NCBIXML._XMLparser-class.html#_secure_name" onclick="show_private();">_secure_name</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>xml.sax.handler.ContentHandler</code></b>:
<code>endDocument</code>,
<code>endElementNS</code>,
<code>endPrefixMapping</code>,
<code>ignorableWhitespace</code>,
<code>processingInstruction</code>,
<code>setDocumentLocator</code>,
<code>skippedEntity</code>,
<code>startDocument</code>,
<code>startElementNS</code>,
<code>startPrefixMapping</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
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">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></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">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">debug</span>=<span class="sig-default">0</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser.__init__">source code</a></span>
</td>
</tr></table>
<p>Constructor</p>
<p>debug - integer, amount of debug information to print</p>
<dl class="fields">
<dt>Overrides:
xml.sax.handler.ContentHandler.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="parse"></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">parse</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">handler</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser.parse">source code</a></span>
</td>
</tr></table>
<p>Parses the XML data</p>
<p>handler -- file handler or StringIO</p>
<p>This method returns a list of Blast record objects.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_end_BlastOutput_program"></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">_end_BlastOutput_program</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_program">source code</a></span>
</td>
</tr></table>
<p>BLAST program, e.g., blastp, blastn, etc.</p>
<p>Save this to put on each blast record object</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_end_BlastOutput_version"></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">_end_BlastOutput_version</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_version">source code</a></span>
</td>
</tr></table>
<p>version number and date of the BLAST engine.</p>
<p>e.g. "BLASTX 2.2.12 [Aug-07-2005]" but there can also be
variants like "BLASTP 2.2.18+" without the date.</p>
<p>Save this to put on each blast record object</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_end_BlastOutput_reference"></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">_end_BlastOutput_reference</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_reference">source code</a></span>
</td>
</tr></table>
<p>a reference to the article describing the algorithm</p>
<p>Save this to put on each blast record object</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_end_BlastOutput_db"></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">_end_BlastOutput_db</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_db">source code</a></span>
</td>
</tr></table>
<p>the database(s) searched</p>
<p>Save this to put on each blast record object</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_end_BlastOutput_query_ID"></a>
<div class="private">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_end_BlastOutput_query_ID</span>(<span class="sig-arg">self</span>)</span>
</h3>
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><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_query_ID">source code</a></span>
</td>
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<p>the identifier of the query</p>
<p>Important in old pre 2.2.14 BLAST, for recent versions
<Iteration_query-ID> is enough</p>
<dl class="fields">
</dl>
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<a name="_end_BlastOutput_query_def"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_end_BlastOutput_query_def</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_query_def">source code</a></span>
</td>
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<p>the definition line of the query</p>
<p>Important in old pre 2.2.14 BLAST, for recent versions
<Iteration_query-def> is enough</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_end_BlastOutput_query_len"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_end_BlastOutput_query_len</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIXML-pysrc.html#BlastParser._end_BlastOutput_query_len">source code</a></span>
</td>
</tr></table>
<p>the length of the query</p>
<p>Important in old pre 2.2.14 BLAST, for recent versions
<Iteration_query-len> is enough</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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