Package Bio :: Package Blast :: Module NCBIWWW
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Module Bio.Blast.NCBIWWW

This module provides code to work with the WWW version of BLAST provided by the NCBI. http://www.ncbi.nlm.nih.gov/BLAST/

Classes: BlastParser Parses output from WWW blast. _Scanner Scans output from NCBI's BLAST WWW server.

Functions: blast Do a BLAST search against the WWW page. (Deprecated) blasturl Do a BLAST search against the stable blasturl. (Deprecated) qblast Do a BLAST search using the QBLAST API.
Classes
BlastParser Parses WWW BLAST data into a Record.Blast object.
_FormParser Parse a form in an HTML page.
_Scanner Scan BLAST output from NCBI's web server at: http://www.ncbi.nlm.nih.gov/BLAST/

Function Summary
  blast(program, database, query, query_from, query_to, entrez_query, filter, expect, word_size, ungapped_alignment, other_advanced, cdd_search, composition_based_statistics, matrix_name, run_psiblast, i_thresh, genetic_code, show_overview, ncbi_gi, format_object, format_type, descriptions, alignments, alignment_view, auto_format, cgi, timeout, output_fn)
blast(program, database, query[, query_from][, query_to] [, entrez_query][, filter][, expect] [, word_size][, other_advanced][, cdd_search] [, composition_based_statistics][, matrix_name][, run_psiblast] [, i_thresh][, genetic_code][, show_overview][, ncbi_gi] [, format_object][, format_type][, descriptions][, alignments] [, alignment_view][, auto_format][, cgi][, timeout]) -> handle
  blasturl(program, datalib, sequence, ncbi_gi, descriptions, alignments, expect, matrix, gap_existence, gap_extend, gapped, filter, html, gcode, path)
blasturl(program, datalib, sequence[, ncbi_gi][, descriptions] [, alignments][, expect][, matrix][, gap_existence][, gap_extend] [, gapped][, filter][, html][, gcode]) -> handle
  qblast(program, database, sequence, ncbi_gi, descriptions, alignments, expect, matrix, filter, format_type, hitlist_size, entrez_query)
Do a BLAST search using the QBLAST server at NCBI.
  _parse_blast_ref_page(handle)
_parse_blast_ref_page(handle, base_cgi) -> cgi, parameters
  _parse_blast_results_page(handle)
_parse_blast_results_page(handle) -> ready, cgi, params
  _parse_qblast_ref_page(handle)
Return tuple of RID, RTOE.
  _send_to_blasturl(query, outhandle)
_send_to_blasturl(query, outhandle)

Function Details

blast(program, database, query, query_from='', query_to='', entrez_query='(none)', filter='L', expect='10', word_size=None, ungapped_alignment='no', other_advanced=None, cdd_search='on', composition_based_statistics=None, matrix_name=None, run_psiblast=None, i_thresh='0.001', genetic_code='1', show_overview='on', ncbi_gi='on', format_object='alignment', format_type='HTML', descriptions='100', alignments='50', alignment_view='Pairwise', auto_format='on', cgi='http://www.ncbi.nlm.nih.gov/blast/Blast.cgi', timeout=20, output_fn=None)

blast(program, database, query[, query_from][, query_to] [, entrez_query][, filter][, expect] [, word_size][, other_advanced][, cdd_search] [, composition_based_statistics][, matrix_name][, run_psiblast] [, i_thresh][, genetic_code][, show_overview][, ncbi_gi] [, format_object][, format_type][, descriptions][, alignments] [, alignment_view][, auto_format][, cgi][, timeout]) -> handle

Blast against the NCBI Blast web page. This uses the NCBI web page cgi script to BLAST, and returns a handle to the results. See:

http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html

for more descriptions about the options.

Required Inputs: o program - The name of the blast program to run (ie. blastn, blastx...) o database - The database to search against (ie. nr, dbest...) o query - The input for the search, which NCBI tries to autodetermine the type of. Ideally, this would be a sequence in FASTA format.

General Options: filter, expect, word_size, other_advanced

Formatting Options: show_overview, ncbi_gi, format_object, format_type, descriptions, alignments, alignment_view, auto_format

Protein specific options: cdd_search, composition_based_statistics, matrix_name, run_psiblast, i_thresh

Translated specific options: genetic code

blasturl(program, datalib, sequence, ncbi_gi=None, descriptions=None, alignments=None, expect=None, matrix=None, gap_existence=None, gap_extend=None, gapped=None, filter=None, html=None, gcode=None, path=None)

blasturl(program, datalib, sequence[, ncbi_gi][, descriptions] [, alignments][, expect][, matrix][, gap_existence][, gap_extend] [, gapped][, filter][, html][, gcode]) -> handle

Do a BLAST search using the stable URL provided by NCBI. program BLASTP, BLASTN, BLASTX, TBLASTN, or TBLASTX. datalib Which database to search against. sequence The sequence to search. ncbi_gi TRUE/FALSE whether to give 'gi' identifier. Def FALSE. descriptions Number of descriptions to show. Def 100. alignments Number of alignments to show. Def 50. expect An expect value cutoff. matrix Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45). gap_existence Give a gap open penalty. gap_extend Give a gap extension penalty. gapped TRUE/FALSE for giving gapped alignments. Def TRUE. filter "none" turns off filtering. Default uses 'seg' or 'dust'. html TRUE/FALSE for html output. Def FALSE. gcode Specify an alternate genetic code for (T)BLASTX.

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

qblast(program, database, sequence, ncbi_gi=None, descriptions=None, alignments=None, expect=None, matrix=None, filter=None, format_type='XML', hitlist_size=None, entrez_query='(none)')

Do a BLAST search using the QBLAST server at NCBI. program BLASTP, BLASTN, BLASTX, TBLASTN, or TBLASTX. database Which database to search against. sequence The sequence to search. ncbi_gi TRUE/FALSE whether to give 'gi' identifier. Def FALSE. 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 Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45). filter "none" turns off filtering. Default uses 'seg' or 'dust'. format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML". entrez_query Entrez query to limit Blast search

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

_parse_blast_ref_page(handle)

_parse_blast_ref_page(handle, base_cgi) -> cgi, parameters

_parse_blast_results_page(handle)

_parse_blast_results_page(handle) -> ready, cgi, params

_parse_qblast_ref_page(handle)

Return tuple of RID, RTOE.

_send_to_blasturl(query, outhandle)

_send_to_blasturl(query, outhandle)

Send a BLAST request to the stable blasturl server at the NCBI. ftp://ncbi.nlm.nih.gov/blast/blasturl/ The results are written to outhandle.

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