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

source code

Code to invoke the NCBI BLAST server over the internet.

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

Functions:
qblast        Do a BLAST search using the QBLAST API.

Functions [hide private]
 
qblast(program, database, sequence, auto_format=None, composition_based_statistics=None, db_genetic_code=None, endpoints=None, entrez_query='(none)', expect=10.0, filter=None, gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None, layout=None, lcase_mask=None, matrix_name=None, nucl_penalty=None, nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None, query_file=None, query_believe_defline=None, query_from=None, query_to=None, searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None, word_size=None, alignments=500, alignment_view=None, descriptions=500, entrez_links_new_window=None, expect_low=None, expect_high=None, format_entrez_query=None, format_object=None, format_type='XML', ncbi_gi=None, results_file=None, show_overview=None, megablast=None)
Do a BLAST search using the QBLAST server at NCBI.
source code
 
_parse_qblast_ref_page(handle)
Extract a tuple of RID, RTOE from the 'please wait' page (PRIVATE).
source code
Variables [hide private]
  __package__ = 'Bio.Blast'
Function Details [hide private]

qblast(program, database, sequence, auto_format=None, composition_based_statistics=None, db_genetic_code=None, endpoints=None, entrez_query='(none)', expect=10.0, filter=None, gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None, layout=None, lcase_mask=None, matrix_name=None, nucl_penalty=None, nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None, query_file=None, query_believe_defline=None, query_from=None, query_to=None, searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None, word_size=None, alignments=500, alignment_view=None, descriptions=500, entrez_links_new_window=None, expect_low=None, expect_high=None, format_entrez_query=None, format_object=None, format_type='XML', ncbi_gi=None, results_file=None, show_overview=None, megablast=None)

source code 
Do a BLAST search using the QBLAST server at NCBI.

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
megablast      TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
service        plain, psi, phi, rpsblast, megablast (lower case)

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/Doc/urlapi.html

_parse_qblast_ref_page(handle)

source code 
Extract a tuple of RID, RTOE from the 'please wait' page (PRIVATE).

The NCBI FAQ pages use TOE for 'Time of Execution', so RTOE is proably
'Request Time of Execution' and RID would be 'Request Identifier'.