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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Blast-module.html">Package Blast</a> ::
Module NCBIWWW
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module NCBIWWW</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Blast.NCBIWWW-pysrc.html">source code</a></span></p>
<p>This module provides code to work with the WWW version of BLAST
provided by the NCBI. http://www.ncbi.nlm.nih.gov/BLAST/</p>
<p>Classes: BlastParser Parses output from WWW blast. _Scanner
Scans output from NCBI's BLAST WWW server.</p>
<p>Functions: qblast Do a BLAST search using the QBLAST API.</p>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIWWW.BlastParser-class.html" class="summary-name">BlastParser</a><br />
Parses WWW BLAST data into a Record.Blast object.
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIWWW._Scanner-class.html" class="summary-name" onclick="show_private();">_Scanner</a><br />
Scan BLAST output from NCBI's web server at:
http://www.ncbi.nlm.nih.gov/BLAST/
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<!-- ==================== FUNCTIONS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIWWW-module.html#qblast" class="summary-sig-name">qblast</a>(<span class="summary-sig-arg">program</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">sequence</span>,
<span class="summary-sig-arg">auto_format</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">composition_based_statistics</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">db_genetic_code</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">endpoints</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">entrez_query</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">(none)</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">expect</span>=<span class="summary-sig-default">10.0</span>,
<span class="summary-sig-arg">filter</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">gapcosts</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">genetic_code</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">hitlist_size</span>=<span class="summary-sig-default">50</span>,
<span class="summary-sig-arg">i_thresh</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">layout</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">lcase_mask</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">matrix_name</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">nucl_penalty</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">nucl_reward</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">other_advanced</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">perc_ident</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">phi_pattern</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">query_file</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">query_believe_defline</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">query_from</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">query_to</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">searchsp_eff</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">service</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">threshold</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">ungapped_alignment</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">word_size</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">alignments</span>=<span class="summary-sig-default">500</span>,
<span class="summary-sig-arg">alignment_view</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">descriptions</span>=<span class="summary-sig-default">500</span>,
<span class="summary-sig-arg">entrez_links_new_window</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">expect_low</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">expect_high</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">format_entrez_query</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">format_object</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">format_type</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">XML</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">ncbi_gi</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">results_file</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">show_overview</span>=<span class="summary-sig-default">None</span>)</span><br />
Do a BLAST search using the QBLAST server at NCBI.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIWWW-pysrc.html#qblast">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_parse_qblast_ref_page"></a><span class="summary-sig-name">_parse_qblast_ref_page</span>(<span class="summary-sig-arg">handle</span>)</span><br />
Return tuple of RID, RTOE.</td>
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<span class="codelink"><a href="Bio.Blast.NCBIWWW-pysrc.html#_parse_qblast_ref_page">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
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<a name="StringTypes"></a><span class="summary-name">StringTypes</span> = <code title="(<type 'str'>, <type 'unicode'>)"><code class="variable-group">(</code><type 'str'><code class="variable-op">, </code><type 'unicode'><code class="variable-group">)</code></code>
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<a name="xml_support"></a><span class="summary-name">xml_support</span> = <code title="1">1</code>
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<!-- ==================== FUNCTION DETAILS ==================== -->
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<a name="qblast"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">qblast</span>(<span class="sig-arg">program</span>,
<span class="sig-arg">database</span>,
<span class="sig-arg">sequence</span>,
<span class="sig-arg">auto_format</span>=<span class="sig-default">None</span>,
<span class="sig-arg">composition_based_statistics</span>=<span class="sig-default">None</span>,
<span class="sig-arg">db_genetic_code</span>=<span class="sig-default">None</span>,
<span class="sig-arg">endpoints</span>=<span class="sig-default">None</span>,
<span class="sig-arg">entrez_query</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">(none)</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">expect</span>=<span class="sig-default">10.0</span>,
<span class="sig-arg">filter</span>=<span class="sig-default">None</span>,
<span class="sig-arg">gapcosts</span>=<span class="sig-default">None</span>,
<span class="sig-arg">genetic_code</span>=<span class="sig-default">None</span>,
<span class="sig-arg">hitlist_size</span>=<span class="sig-default">50</span>,
<span class="sig-arg">i_thresh</span>=<span class="sig-default">None</span>,
<span class="sig-arg">layout</span>=<span class="sig-default">None</span>,
<span class="sig-arg">lcase_mask</span>=<span class="sig-default">None</span>,
<span class="sig-arg">matrix_name</span>=<span class="sig-default">None</span>,
<span class="sig-arg">nucl_penalty</span>=<span class="sig-default">None</span>,
<span class="sig-arg">nucl_reward</span>=<span class="sig-default">None</span>,
<span class="sig-arg">other_advanced</span>=<span class="sig-default">None</span>,
<span class="sig-arg">perc_ident</span>=<span class="sig-default">None</span>,
<span class="sig-arg">phi_pattern</span>=<span class="sig-default">None</span>,
<span class="sig-arg">query_file</span>=<span class="sig-default">None</span>,
<span class="sig-arg">query_believe_defline</span>=<span class="sig-default">None</span>,
<span class="sig-arg">query_from</span>=<span class="sig-default">None</span>,
<span class="sig-arg">query_to</span>=<span class="sig-default">None</span>,
<span class="sig-arg">searchsp_eff</span>=<span class="sig-default">None</span>,
<span class="sig-arg">service</span>=<span class="sig-default">None</span>,
<span class="sig-arg">threshold</span>=<span class="sig-default">None</span>,
<span class="sig-arg">ungapped_alignment</span>=<span class="sig-default">None</span>,
<span class="sig-arg">word_size</span>=<span class="sig-default">None</span>,
<span class="sig-arg">alignments</span>=<span class="sig-default">500</span>,
<span class="sig-arg">alignment_view</span>=<span class="sig-default">None</span>,
<span class="sig-arg">descriptions</span>=<span class="sig-default">500</span>,
<span class="sig-arg">entrez_links_new_window</span>=<span class="sig-default">None</span>,
<span class="sig-arg">expect_low</span>=<span class="sig-default">None</span>,
<span class="sig-arg">expect_high</span>=<span class="sig-default">None</span>,
<span class="sig-arg">format_entrez_query</span>=<span class="sig-default">None</span>,
<span class="sig-arg">format_object</span>=<span class="sig-default">None</span>,
<span class="sig-arg">format_type</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">XML</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">ncbi_gi</span>=<span class="sig-default">None</span>,
<span class="sig-arg">results_file</span>=<span class="sig-default">None</span>,
<span class="sig-arg">show_overview</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIWWW-pysrc.html#qblast">source code</a></span>
</td>
</tr></table>
<p>Do a BLAST search using the QBLAST server at NCBI.</p>
<p>Supports all parameters of the qblast API for Put and Get. Some useful
parameters: program blastn, blastp, blastx, tblastn, or tblastx
(lower case) database Which database to search against (e.g.
"nr"). sequence The sequence to search. ncbi_gi
TRUE/FALSE whether to give 'gi' identifier. descriptions Number of
descriptions to show. Def 500. alignments Number of alignments to
show. Def 500. expect An expect value cutoff. Def 10.0.
matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
filter "none" turns off filtering. Default no
filtering format_type "HTML", "Text",
"ASN.1", or "XML". Def. "XML".
entrez_query Entrez query to limit Blast search hitlist_size Number
of hits to return. Default 50</p>
<p>This function does no checking of the validity of the parameters and
passes the values to the server as is. More help is available at:
http://www.ncbi.nlm.nih.gov/BLAST/blast_overview.html</p>
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