[Bioperl-l] update to bp_remote_blast.pl

[Brian Osborne]

Evan,

Added update.

Brian O.


On 3/15/06 11:21 AM, "Evan" <eweaver at gmail.com> wrote:

> #!/usr/local/bin/perl -w
> # BioPerl module for remote_blast.pl
> #
> # Revived by Evan Weaver for bioperl-1.5.1
> # 3/14/2006
> #
> # Copyright Jason Stajich, Evan Weaver
> #
> # You may distribute this module under the same terms as perl itself
> 
> # POD documentation - main docs after the code
> 
> use strict;
> use vars qw($USAGE);
> 
> use Bio::Tools::Run::RemoteBlast;
> use Bio::SeqIO;
> use Getopt::Long;
> 
> $USAGE = "remote_blast.pl [-h] [-p prog] [-d db] [-e expect] [-mod
> Blast] [-f seqformat] -z=\"entrez query\" -v 1 -t output_format -i
> seqfile\n";
> 
> my ($prog, $db, $expect,$method) = ( 'blastp', 'nr', '10', 'Blast');
> 
> my ($sequencefile,$sequenceformat,$help, $entrez, $outputformat,
> $verbose) = (undef, 'fasta',undef, undef, undef, 1);
> 
> &GetOptions('prog|p=s'               => \$prog,
>    'db|d=s'                 => \$db,
>    'expect|e=s'             => \$expect,
>    'blsmod|module|method=s' => \$method,
>    'input|i=s'              => \$sequencefile,   
>    'format|f=s'             => \$sequenceformat,
>    'help|h'                 => \$help,
>    'entrez|z=s'             => \$entrez,
>    'output_format|t=s'      => \$outputformat,
>    'verbose|v=s'            => \$verbose
>    );
> 
> if( $help ) {
>     exec('perldoc', $0);
>     die;
> }
> 
> if( !defined $prog ) {
>     die($USAGE . "\n\tMust specify a valid program name ([t]blast[pxn])\n");
> }
> if( !defined $db ) {
>     die($USAGE . "\n\tMust specify a db to search\n");
> }
> if( !defined $sequencefile ) {
>     die($USAGE . "\n\tMust specify an input file\n");
> }
> 
> my $blastfactory = new Bio::Tools::Run::RemoteBlast ('-prog'      => $prog,
>     '-data'      => $db,
>     '-expect'    => $expect,
>     'readmethod' => $method,
>     );
> 
> if ($entrez) {
>   if ($verbose) {
>     print "Entrez query (submission side): $entrez\n";
>   }
>   #$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{ FORMAT_ENTREZ_QUERY
> } = $entrez;
>   $Bio::Tools::Run::RemoteBlast::HEADER{ ENTREZ_QUERY } = $entrez;
> 
> }
> if ($outputformat) {
>   print "Don't use output format type; it doesn't work.\n";
>   $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{ FORMAT_TYPE } =
> $outputformat;
> }
> 
> # submit_blast can only currenly handle fasta format files so I'll
> # preprocess outside of the module but I'd rather be sure here
> 
> my $input;
> if( $sequenceformat !~ /fasta/ ) {
>     my @seqs;
>     my $seqio = new Bio::SeqIO('-format' => $sequenceformat,
>       '-file'   => $sequencefile );
>     while( my $seq = $seqio->next_seq() ) {
> push @seqs, $seq;
>     }
>     $input = \@seqs;
> } else {
>     $input = $sequencefile;
> }
> 
> my $r = $blastfactory->submit_blast($input);
> #my $r = $factory->submit_blast(?amino.fa?);
> 
> print STDERR "waiting...\n" if( $verbose > 0 );
> while ( my @rids = $blastfactory->each_rid ) {
>   foreach my $rid ( @rids ) {
>     my $rc = $blastfactory->retrieve_blast($rid);
>     if( !ref($rc) ) {
>       if( $rc < 0 ) {
>         $blastfactory->remove_rid($rid);
>       }
>       print STDERR "   checking $rid\n" if ( $verbose > 0 );
>       sleep 5;
>     } else {
>       my $result = $rc->next_result();
>       #save the output
>       my $filename = $result->query_name()."\.out";
>       $blastfactory->save_output($filename);
>       $blastfactory->remove_rid($rid);
>       print "\nQuery Name: ", $result->query_name(), "\n";
>       while ( my $hit = $result->next_hit ) {
>         next unless ( $verbose > 0);
>         print "\thit name is ", $hit->name, "\n";
>         while( my $hsp = $hit->next_hsp ) {
>           print "\t\tscore is ", $hsp->score, "\n";
>         }
>       }
>     }
>   }
>   print STDERR scalar(@rids) . " left\n";
> }
> 
> 
> __END__
> 
> #
> # BioPerl module for remote_blast.pl
> #
> # Cared for by Jason Stajich <jason-at-bioperl-dot-org>
> #
> # Copyright Jason Stajich
> #
> # You may distribute this module under the same terms as perl itself
> 
> # POD documentation - main docs before the code
> 
> =head1 NAME
> 
> remote_blast.pl - script for submitting jobs to a remote blast server
> (ncbi blast queue at this time)
> 
> =head1 SYNOPSIS
> 
> % remote_blast.pl -p blastp -d ecoli -e 1e-5 -i myseqs.fa
> 
> =head1 DESCRIPTION
> 
> This module will run a remote blast on a set of sequences by
> submitting them to the NCBI blast queue and printing the output of the
> request.
> 
> =head1 FEEDBACK
> 
> =head2 Mailing Lists
> 
> User feedback is an integral part of the evolution of this and other
> Bioperl modules. Send your comments and suggestions preferably to
> the Bioperl mailing list.  Your participation is much appreciated.
> 
>   bioperl-l at bioperl.org               - General discussion
>   http://bioperl.org/MailList.shtml   - About the mailing lists
> 
> =head2 Reporting Bugs
> 
> Report bugs to the Bioperl bug tracking system to help us keep track
> the bugs and their resolution.  Bug reports can be submitted via the
> web:
> 
>   http://bugzilla.open-bio.org/
> 
> =head1 AUTHOR - Jason Stajich
> 
> Email jason-at-bioperl-dot-org
> 
> =cut