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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-09-22 13:39:48 UTC
  • mfrom: (3.1.11 sid)
  • Revision ID: package-import@ubuntu.com-20130922133948-c6z62zegjyp7ztou
Tags: 1.6.922-1
http://bugs.debian.org/722910
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
  Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

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scripts/searchio/bp_search2table.pl
 
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#!/usr/bin/perl
 
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=head1 NAME
 
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bp_search2table - turn SearchIO parseable reports into tab delimited format like NCBI's -m 9 
 
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=head1 SYNOPSIS
 
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  bp_search2table -f fasta -i file.FASTA -o output.table
 
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=head1 DESCRIPTION 
 
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Turn SearchIO reports into a tabular format like NCBI's -m 9 output.
 
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=head1 FEEDBACK
 
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=head2 Mailing Lists
 
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User feedback is an integral part of the evolution of this and other
 
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Bioperl modules. Send your comments and suggestions preferably to
 
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the Bioperl mailing list.  Your participation is much appreciated.
 
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  bioperl-l@bioperl.org                  - General discussion
 
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  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
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=head2 Reporting Bugs
 
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Report bugs to the Bioperl bug tracking system to help us keep track
 
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of the bugs and their resolution. Bug reports can be submitted via
 
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email or the web:
 
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  https://redmine.open-bio.org/projects/bioperl/
 
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=head1 AUTHOR
 
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  Jason Stajich jason_at_bioperl-dot-org
 
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=cut
 
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use strict;
 
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use warnings;
 
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use Bio::SearchIO;
 
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use Getopt::Long;
 
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my ($format, $file,$output) = ('blast');
 
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GetOptions(
 
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           'f|format:s'   => \$format,
 
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           'i|input:s'    => \$file,
 
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           'o|output:s'   => \$output);
 
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if( @ARGV ) { 
 
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    $file = shift;
 
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}
 
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my $in = Bio::SearchIO->new(-format => $format,
 
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                            -file   => $file);
 
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my $out;
 
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if( $output ) { 
 
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    open($out,">$output") || die "cannot open $output for writing";
 
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} else { 
 
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    $out = \*STDOUT;
 
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}
 
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while( my $r = $in->next_result ) {
 
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    while( my $hit = $r->next_hit ) {
 
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        while( my $hsp = $hit->next_hsp ) {
 
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            my $mismatchcount = $hsp->length('total') - 
 
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                ($hsp->num_conserved + $hsp->gaps('total'));
 
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            print $out join("\t", ( $r->query_name,
 
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                                    $hit->name,
 
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                                    sprintf("%.2f",$hsp->percent_identity),
 
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                                    $hsp->length('total'),
 
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                                    $mismatchcount,
 
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                                    $hsp->gaps('total'),
 
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                                    # flip start/end on rev strand
 
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                                    $hsp->query->strand < 0 ?
 
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                                    ( $hsp->query->end,
 
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                                      $hsp->query->start ) :
 
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                                    ( $hsp->query->start,
 
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                                      $hsp->query->end ),
 
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                                    $hsp->hit->strand < 0 ?
 
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                                    ( $hsp->hit->end,
 
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                                      $hsp->hit->start ) :
 
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                                    ( $hsp->hit->start,
 
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                                      $hsp->hit->end ),
 
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                                    $hsp->evalue,
 
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                                    # chance this to $hsp->sw_score 
 
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                                    # if you would rather have that
 
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                                    # it will only work for FASTA parsing though!
 
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                                    $hsp->bits)),"\n";
 
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        }
 
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    }
 
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}