[Bioperl-l] Remote Blast and Report
SMarkel at accelrys.com
Wed Feb 25 21:04:29 EST 2009
There's a polling mechanism you need to use. See the example in the
Bio::Tools::Run::RemoteBlast module. Start looking around line 60.
Scott Markel, Ph.D.
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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ocar Campos
> Sent: Wednesday, 25 February 2009 4:04 PM
> To: Bioperl Mailing List.
> Subject: [Bioperl-l] Remote Blast and Report
> I'm working in a script to remote blast a file with some sequences, I
> already got the part of sending the query to blast, but I do not get the
> idea of how retrieve a txt report, I mean, like the one you get by running
> blast via web and you can read in a plane text editor.
> This is what I've done so far:
> use Bio::Tools::Run::RemoteBlast;
> use Bio::SearchIO;
> $prog = "tblastx";
> $db = "nr";
> $e_val = "1e-10";
> $remoteBlast = Bio::Tools::Run::RemoteBlast->new(-prog => $prog,
> -data => $db,
> -expect => $e_val
> -readmethod => 'Blast');
> #I select the file to make que query and do the blast.
> $infile = 'file.input.fasta';
> $r = $remoteBlast->submit_blast($infile);
> #this should be the report i get.
> $outfile = 'got.output';
> further than this I've tried some things but none of them work, anybody
> could give an idea of how retrieving the plane text reports please?
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