[BioPython] PHI-BLAST support?

[Brad Chapman]

Hi Pål;

> I'm wondering whether BioPython supports doing PHI-BLAST searches (locally), 
>
> btw, here's the command I issue to run PHI-BLAST from command-line:
> 
>     blastpgp -i [infile] -k [patternfile] -p patseedp

Yes, we do support that. If you had your infile in a variable
'input_file' and your patternfile in a variable 'pattern_file',
then you could do the search against, say, a local swissprot
database with:

from Bio.Blast import NCBIStandalone

result_handle, error_handle = NCBIStandalone.blastpgp(
        "/usr/local/bin/blastpgp", "swissprot", input_file,
        program = "patseedp", hit_infile = pattern_file)

The variable result_handle contains the output of this run, and
error_handle any errors that may have occurred.

> and whether parsing of PHI-BLAST output information such as pattern positions
> is supported (see below)?

I don't believe the BLAST parser currently supports output from
PHI-BLAST searches. We'd certainly accept contributions towards this
goal.

Hope this helps!
Brad