/usr/bin/bp_search2BSML is in bioperl 1.6.901-2.
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 | #!/usr/bin/perl -w
eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
if 0; # not running under some shell
# Author: Jason Stajich <jason-at-bioperl-dot-org>
# Description: Turn SearchIO parseable report(s) into a GFF report
#
=head1 NAME
search2bsml - Turn SearchIO parseable reports(s) into a BSML report
=head1 SYNOPSIS
Usage:
search2bsml [-o outputfile] [-f reportformat] [-i inputfilename] OR file1 file2 ..
=head1 DESCRIPTION
This script will turn a protein Search report (BLASTP, FASTP, SSEARCH,
AXT, WABA, SIM4) into a BSML File.
The options are:
-i infilename - (optional) inputfilename, will read
either ARGV files or from STDIN
-o filename - the output filename [default STDOUT]
-f format - search result format (blast, fasta,waba,axt)
(ssearch is fasta format). default is blast.
-h - this help menu
Additionally specify the filenames you want to process on the
command-line. If no files are specified then STDIN input is assumed.
You specify this by doing: search2gff E<lt> file1 file2 file3
=head1 AUTHOR
Jason Stajich, jason-at-bioperl-dot-org
=cut
use strict;
use Getopt::Long;
use Bio::SearchIO;
my ($output,$input,$format,$type,$help,$cutoff);
$format = 'blast'; # by default
GetOptions(
'i|input:s' => \$input,
'o|output:s' => \$output,
'f|format:s' => \$format,
'c|cutoff:s' => \$cutoff,
'h|help' => sub{ exec('perldoc',$0);
exit(0)
},
);
# if no input is provided STDIN will be used
my $parser = new Bio::SearchIO(-format => $format,
-file => $input);
my $out;
if( defined $output ) {
$out = new Bio::SearchIO(-file => ">$output",
-output_format => 'BSMLResultWriter');
} else {
$out = new Bio::SearchIO(-output_format => 'BSMLResultWriter'); # STDOUT
}
while( my $result = $parser->next_result ) {
$out->write_result($result);
}
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