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#!/usr/bin/perl -w
# $Id: search2BSML.PLS,v 1.2 2005/04/26 15:03:53 jason Exp $
# Author:      Jason Stajich <jason-at-bioperl-dot-org>
# Description: Turn SearchIO parseable report(s) into a GFF report
HideShow 33 lines of Pod
#
=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);
}