/usr/bin/bp_remote_blast is in bioperl 1.6.924-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
#
# BioPerl module for bp_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 warnings;
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 bp_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
bp_remote_blast.pl - script for submitting jobs to a remote blast server
(ncbi blast queue at this time)
=head1 SYNOPSIS
% bp_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@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - 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:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=cut
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