[Biopython-dev] Small change to NCBIWWW

[Brad Chapman]

Hello all;
I was using NCBIWWW.blast() to access the BLAST cgi script this
morning and noticed that the parameters used to restrict the organism
type to BLAST against weren't quite working right. The gi_list
variable was included as a dictionary parameter, but wasn't actually
being passed to the CGI script. 

Attached is a patch which fixes this (oooh, one line fix! Very
impressive :-). and also adds support for the LIST_ORG box in which
you can specify an arbitrary organism to blast against (ie. other
organisms that aren't in their pull down box).

Let me know if anything doesn't seem right with this. Both options now 
seem to work fine for me. Thanks!

Brad


-------------- next part --------------
*** NCBIWWW.py.orig	Thu Oct 19 21:31:54 2000
--- NCBIWWW.py	Sun Nov 19 11:54:59 2000
***************
*** 531,537 ****
  
  def blast(program, datalib, sequence,
            input_type='Sequence in FASTA format',
!           double_window=None, gi_list='(None)', expect='10',
            filter='L', genetic_code='Standard (1)',
            mat_param='PAM30     9       1',
            other_advanced=None, ncbi_gi=None, overview=None,
--- 531,538 ----
  
  def blast(program, datalib, sequence,
            input_type='Sequence in FASTA format',
!           double_window=None, gi_list='(None)',
!           list_org = None, expect='10',
            filter='L', genetic_code='Standard (1)',
            mat_param='PAM30     9       1',
            other_advanced=None, ncbi_gi=None, overview=None,
***************
*** 542,548 ****
            ):
      """blast(program, datalib, sequence,
      input_type='Sequence in FASTA format',
!     double_window=None, gi_list='(None)', expect='10',
      filter='L', genetic_code='Standard (1)',
      mat_param='PAM30     9       1',
      other_advanced=None, ncbi_gi=None, overview=None,
--- 543,550 ----
            ):
      """blast(program, datalib, sequence,
      input_type='Sequence in FASTA format',
!     double_window=None, gi_list='(None)',
!     list_org = None, expect='10',
      filter='L', genetic_code='Standard (1)',
      mat_param='PAM30     9       1',
      other_advanced=None, ncbi_gi=None, overview=None,
***************
*** 570,575 ****
--- 572,579 ----
                'DATALIB' : datalib,
                'SEQUENCE' : sequence,
                'DOUBLE_WINDOW' : double_window,
+               'GI_LIST' : gi_list,
+               'LIST_ORG' : list_org,
                'INPUT_TYPE' : input_type,
                'EXPECT' : expect,
                'FILTER' : filter,