Package Bio :: Package Blast :: Module NCBIWWW
[hide private]
[frames] | no frames]

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 [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'.