[BioPython] qblast + documentation

[Michael S. Robeson]

> http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/ 
> Blast/NCBIWWW.py?rev=1.46&cvsroot=biopython&content-type=text/ 
> vnd.viewcvs-markup
Are those new parameters? They do exist in the code I downloaded?  
Guess I will download again from fink.

> If you are familiar with the BLAST terminology this is probably  
> very obvious, but you need to set the NUCL_REWARD and NUCL_PENALTY  
> options in the URL.

Yeah, I did not mean to say it was biopython's fault, but the version  
of the code I have had no parameters under qblast for me to alter  
after we new there was a difference with the web interface end at  
NCBI. The version I have (latest via fink, biopython version:  
1.43-1001) showed this:

def 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)',
            ):

and not:

def 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
            ):

So, there must be a problem with my fink installation or something. I  
will try and uninstall and re-install biopython via fink.

-Mike