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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Blast-module.html">Package Blast</a> ::
Module NCBIStandalone
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module NCBIStandalone</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html">source code</a></span></p>
<p>This module provides code to work with the standalone version of
BLAST, either blastall or blastpgp, provided by the NCBI.
http://www.ncbi.nlm.nih.gov/BLAST/</p>
<p>Classes: LowQualityBlastError Except that indicates low quality
query sequences. BlastParser Parses output from blast.
BlastErrorParser Parses output and tries to diagnose possible
errors. PSIBlastParser Parses output from psi-blast. Iterator
Iterates over a file of blast results.</p>
<p>_Scanner Scans output from standalone BLAST.
_BlastConsumer Consumes output from blast. _PSIBlastConsumer
Consumes output from psi-blast. _HeaderConsumer Consumes header
information. _DescriptionConsumer Consumes description information.
_AlignmentConsumer Consumes alignment information. _HSPConsumer
Consumes hsp information. _DatabaseReportConsumer Consumes database
report information. _ParametersConsumer Consumes parameters
information.</p>
<p>Functions: blastall Execute blastall. blastpgp Execute
blastpgp. rpsblast Execute rpsblast.</p>
<!-- ==================== CLASSES ==================== -->
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone.LowQualityBlastError-class.html" class="summary-name">LowQualityBlastError</a><br />
Error caused by running a low quality sequence through BLAST.
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone.ShortQueryBlastError-class.html" class="summary-name">ShortQueryBlastError</a><br />
Error caused by running a short query sequence through BLAST.
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone._Scanner-class.html" class="summary-name" onclick="show_private();">_Scanner</a><br />
Scan BLAST output from blastall or blastpgp.
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone.BlastParser-class.html" class="summary-name">BlastParser</a><br />
Parses BLAST data into a Record.Blast object.
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone.PSIBlastParser-class.html" class="summary-name">PSIBlastParser</a><br />
Parses BLAST data into a Record.PSIBlast object.
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone._HeaderConsumer-class.html" class="summary-name" onclick="show_private();">_HeaderConsumer</a>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html" class="summary-name" onclick="show_private();">_DescriptionConsumer</a>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html" class="summary-name" onclick="show_private();">_AlignmentConsumer</a>
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<span class="summary-type"> </span>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html" class="summary-name" onclick="show_private();">_DatabaseReportConsumer</a>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone._ParametersConsumer-class.html" class="summary-name" onclick="show_private();">_ParametersConsumer</a>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" class="summary-name" onclick="show_private();">_BlastConsumer</a>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" class="summary-name" onclick="show_private();">_PSIBlastConsumer</a>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone.Iterator-class.html" class="summary-name">Iterator</a><br />
Iterates over a file of multiple BLAST results.
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" class="summary-name" onclick="show_private();">_BlastErrorConsumer</a>
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<span class="summary-type"> </span>
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<a href="Bio.Blast.NCBIStandalone.BlastErrorParser-class.html" class="summary-name">BlastErrorParser</a><br />
Attempt to catch and diagnose BLAST errors while parsing.
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<!-- ==================== FUNCTIONS ==================== -->
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<span class="summary-type">read, error Undohandles</span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIStandalone-module.html#blastall" class="summary-sig-name">blastall</a>(<span class="summary-sig-arg">blastcmd</span>,
<span class="summary-sig-arg">program</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">infile</span>,
<span class="summary-sig-arg">align_view</span>=<span class="summary-sig-default">'7'</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Execute and retrieve data from blastall.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#blastall">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">read, error Undohandles</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Blast.NCBIStandalone-module.html#blastpgp" class="summary-sig-name">blastpgp</a>(<span class="summary-sig-arg">blastcmd</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">infile</span>,
<span class="summary-sig-arg">align_view</span>=<span class="summary-sig-default">'7'</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Execute and retrieve data from blastpgp.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#blastpgp">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">read, error Undohandles</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.Blast.NCBIStandalone-module.html#rpsblast" class="summary-sig-name">rpsblast</a>(<span class="summary-sig-arg">blastcmd</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">infile</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Execute and retrieve data from standalone RPS-BLAST.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#rpsblast">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_re_search"></a><span class="summary-sig-name">_re_search</span>(<span class="summary-sig-arg">regex</span>,
<span class="summary-sig-arg">line</span>,
<span class="summary-sig-arg">error_msg</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_re_search">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_cols"></a><span class="summary-sig-name">_get_cols</span>(<span class="summary-sig-arg">line</span>,
<span class="summary-sig-arg">cols_to_get</span>,
<span class="summary-sig-arg">ncols</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">expected</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span></td>
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<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_get_cols">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_safe_int"></a><span class="summary-sig-name">_safe_int</span>(<span class="summary-sig-arg">str</span>)</span></td>
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<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_safe_int">source code</a></span>
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<span class="summary-type"> </span>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_safe_float"></a><span class="summary-sig-name">_safe_float</span>(<span class="summary-sig-arg">str</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_safe_float">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Blast.NCBIStandalone-module.html#_security_check_parameters" class="summary-sig-name" onclick="show_private();">_security_check_parameters</a>(<span class="summary-sig-arg">param_dict</span>)</span><br />
Look for any attempt to insert a command into a parameter.</td>
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<span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_security_check_parameters">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
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<td align="left"><span class="table-header">Variables</span></td>
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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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<span class="summary-type"> </span>
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<a name="xml_support"></a><span class="summary-name">xml_support</span> = <code title="1">1</code>
</td>
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<!-- ==================== FUNCTION DETAILS ==================== -->
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<a name="blastall"></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">blastall</span>(<span class="sig-arg">blastcmd</span>,
<span class="sig-arg">program</span>,
<span class="sig-arg">database</span>,
<span class="sig-arg">infile</span>,
<span class="sig-arg">align_view</span>=<span class="sig-default">'7'</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#blastall">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Execute and retrieve data from blastall. blastcmd is the command
used to launch the 'blastall' executable. program is the blast program
to use, e.g. 'blastp', 'blastn', etc. database is the path to the database
to search against. infile is the path to the file containing
the sequence to search with.
You may pass more parameters to **keywds to change the behavior of
the search. Otherwise, optional values will be chosen by blastall.
The Blast output is by default in XML format. Use the align_view keyword
for output in a different format.
Scoring
matrix Matrix to use.
gap_open Gap open penalty.
gap_extend Gap extension penalty.
nuc_match Nucleotide match reward. (BLASTN)
nuc_mismatch Nucleotide mismatch penalty. (BLASTN)
query_genetic_code Genetic code for Query.
db_genetic_code Genetic code for database. (TBLAST[NX])
Algorithm
gapped Whether to do a gapped alignment. T/F (not for TBLASTX)
expectation Expectation value cutoff.
wordsize Word size.
strands Query strands to search against database.([T]BLAST[NX])
keep_hits Number of best hits from a region to keep.
xdrop Dropoff value (bits) for gapped alignments.
hit_extend Threshold for extending hits.
region_length Length of region used to judge hits.
db_length Effective database length.
search_length Effective length of search space.
Processing
filter Filter query sequence for low complexity (with SEG)? T/F
believe_query Believe the query defline. T/F
restrict_gi Restrict search to these GI's.
nprocessors Number of processors to use.
oldengine Force use of old engine T/F
Formatting
html Produce HTML output? T/F
descriptions Number of one-line descriptions.
alignments Number of alignments.
align_view Alignment view. Integer 0-11,
passed as a string or integer.
show_gi Show GI's in deflines? T/F
seqalign_file seqalign file to output.
</pre>
<dl class="fields">
<dt>Returns: read, error Undohandles</dt>
</dl>
</td></tr></table>
</div>
<a name="blastpgp"></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">blastpgp</span>(<span class="sig-arg">blastcmd</span>,
<span class="sig-arg">database</span>,
<span class="sig-arg">infile</span>,
<span class="sig-arg">align_view</span>=<span class="sig-default">'7'</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#blastpgp">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Execute and retrieve data from blastpgp. blastcmd is the command
used to launch the 'blastpgp' executable. database is the path to the
database to search against. infile is the path to the file containing
the sequence to search with.
You may pass more parameters to **keywds to change the behavior of
the search. Otherwise, optional values will be chosen by blastpgp.
The Blast output is by default in XML format. Use the align_view keyword
for output in a different format.
Scoring
matrix Matrix to use.
gap_open Gap open penalty.
gap_extend Gap extension penalty.
window_size Multiple hits window size.
npasses Number of passes.
passes Hits/passes. Integer 0-2.
Algorithm
gapped Whether to do a gapped alignment. T/F
expectation Expectation value cutoff.
wordsize Word size.
keep_hits Number of beset hits from a region to keep.
xdrop Dropoff value (bits) for gapped alignments.
hit_extend Threshold for extending hits.
region_length Length of region used to judge hits.
db_length Effective database length.
search_length Effective length of search space.
nbits_gapping Number of bits to trigger gapping.
pseudocounts Pseudocounts constants for multiple passes.
xdrop_final X dropoff for final gapped alignment.
xdrop_extension Dropoff for blast extensions.
model_threshold E-value threshold to include in multipass model.
required_start Start of required region in query.
required_end End of required region in query.
Processing
XXX should document default values
program The blast program to use. (PHI-BLAST)
filter Filter query sequence for low complexity (with SEG)? T/F
believe_query Believe the query defline? T/F
nprocessors Number of processors to use.
Formatting
html Produce HTML output? T/F
descriptions Number of one-line descriptions.
alignments Number of alignments.
align_view Alignment view. Integer 0-11,
passed as a string or integer.
show_gi Show GI's in deflines? T/F
seqalign_file seqalign file to output.
align_outfile Output file for alignment.
checkpoint_outfile Output file for PSI-BLAST checkpointing.
restart_infile Input file for PSI-BLAST restart.
hit_infile Hit file for PHI-BLAST.
matrix_outfile Output file for PSI-BLAST matrix in ASCII.
_security_check_parameters(keywds)
align_infile Input alignment file for PSI-BLAST restart.
</pre>
<dl class="fields">
<dt>Returns: read, error Undohandles</dt>
</dl>
</td></tr></table>
</div>
<a name="rpsblast"></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">rpsblast</span>(<span class="sig-arg">blastcmd</span>,
<span class="sig-arg">database</span>,
<span class="sig-arg">infile</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#rpsblast">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Execute and retrieve data from standalone RPS-BLAST. blastcmd is the
command used to launch the 'rpsblast' executable. database is the path
to the database to search against. infile is the path to the file
containing the sequence to search with.
You may pass more parameters to **keywds to change the behavior of
the search. Otherwise, optional values will be chosen by rpsblast.
Please note that this function will give XML output by default, by
setting align_view to seven (i.e. command line option -m 7).
You should use the NCBIXML.parse() function to read the resulting output.
This is because NCBIStandalone.BlastParser() does not understand the
plain text output format from rpsblast.
WARNING - The following text and associated parameter handling has not
received extensive testing. Please report any errors we might have made...
Algorithm/Scoring
gapped Whether to do a gapped alignment. T/F
multihit 0 for multiple hit (default), 1 for single hit
expectation Expectation value cutoff.
range_restriction Range restriction on query sequence (Format: start,stop) blastp only
0 in 'start' refers to the beginning of the sequence
0 in 'stop' refers to the end of the sequence
Default = 0,0
xdrop Dropoff value (bits) for gapped alignments.
xdrop_final X dropoff for final gapped alignment (in bits).
xdrop_extension Dropoff for blast extensions (in bits).
search_length Effective length of search space.
nbits_gapping Number of bits to trigger gapping.
protein Query sequence is protein. T/F
db_length Effective database length.
Processing
filter Filter query sequence for low complexity? T/F
case_filter Use lower case filtering of FASTA sequence T/F, default F
believe_query Believe the query defline. T/F
nprocessors Number of processors to use.
logfile Name of log file to use, default rpsblast.log
Formatting
html Produce HTML output? T/F
descriptions Number of one-line descriptions.
alignments Number of alignments.
align_view Alignment view. Integer 0-11,
_security_check_parameters(keywds)
passed as a string or integer.
show_gi Show GI's in deflines? T/F
seqalign_file seqalign file to output.
align_outfile Output file for alignment.
</pre>
<dl class="fields">
<dt>Returns: read, error Undohandles</dt>
</dl>
</td></tr></table>
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<a name="_security_check_parameters"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_security_check_parameters</span>(<span class="sig-arg">param_dict</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_security_check_parameters">source code</a></span>
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<p>Look for any attempt to insert a command into a parameter.</p>
<p>e.g. blastall(..., matrix='IDENTITY -F 0; rm -rf /etc/passwd')</p>
<p>Looks for ";" or "&&" in the strings (Unix
and Windows syntax for appending a command line), and if found raises an
exception.</p>
<dl class="fields">
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