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Viewing changes to Bio/SearchIO/hmmer.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Lines of Context:
Bio/SearchIO/hmmer.pm
1
 
# $Id: hmmer.pm,v 1.34.4.1 2006/10/02 23:10:26 sendu Exp $
 
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# $Id: hmmer.pm 15005 2008-11-19 20:32:50Z dave_messina $
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#
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# BioPerl module for Bio::SearchIO::hmmer
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#
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    # do not use this class directly it is available through Bio::SearchIO
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    use Bio::SearchIO;
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    my $in = new Bio::SearchIO(-format => 'hmmer',
 
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    my $in = Bio::SearchIO->new(-format => 'hmmer',
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                               -file   => 't/data/L77119.hmmer');
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    while( my $result = $in->next_result ) {
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        # this is a Bio::Search::Result::HMMERResult object
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=head2 new
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 Title   : new
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 Usage   : my $obj = new Bio::SearchIO::hmmer();
 
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 Usage   : my $obj = Bio::SearchIO::hmmer->new();
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 Function: Builds a new Bio::SearchIO::hmmer object 
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 Returns : Bio::SearchIO::hmmer
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 Args    : -fh/-file => HMMER filename
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                            $prelength = CORE::length($1);
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                            $width     = 0;
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                            # $width = CORE::length($2);
 
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                            # deal with fact that start en stop is on same line
 
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                            my $data = $2;
 
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                            if ($data =~ s/\<\-?\*?\s*$//)
 
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                            {
 
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                                $width = CORE::length($data);
 
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                            }
 
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                            $self->element(
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                                {
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                                    'Name' => 'Hsp_qseq',
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                                    'Data' => $2
 
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                                    'Data' => $data
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                                }
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                            );
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                            $count       = 0;
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                                );
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                            }
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                            else {
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                                $self->debug("midline is $_\n")
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                                  if ( $verbose > 0
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                                    && CORE::length($_) <= $prelength );
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                                $self->element(
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                                    {
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                                        'Name' => 'Hsp_midline',
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                        || ( $count != 1
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                            && /^\s+RF\s+[x\s]+$/o )
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                      );
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                    $self->debug("$count $_") if $verbose > 0;
 
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                    # fix for bug 2632
 
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                    next if ($_ =~ m/^\s+CS\s+/o && $count == 0);
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                    if ( /^Histogram/o || m!^//!o || /^Query sequence/o ) {
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                        if ( $self->in_element('hsp') ) {
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                            $self->end_element( { 'Name' => 'Hsp' } );
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                                'Name' => 'Hsp_identity',
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                                'Data' => 0
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                            }
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                        );
 
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                        );                     
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                        $self->element(
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                            {
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                                'Name' => 'Hsp_positive',
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                            $prelength = CORE::length($1);
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                            $width     = 0;
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                            # $width = CORE::length($2);
 
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                            # deal with fact that start en stop is on same line
 
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                            my $data = $2;
 
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                            if ($data =~ s/\<\-?\*?\s*$//)
 
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                            {
 
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                              $width = CORE::length($data);
 
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                            }
 
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                            $self->element(
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                                {
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                                    'Name' => 'Hsp_hseq',
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                                    'Data' => $2
 
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                                    'Data' => $data
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                                }
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                            );
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                            $count       = 0;
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                            'Name' => 'Hsp_query-from',
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                            'Data' => shift @$HSPinfo
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                        }
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                    );
 
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                    );                    
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                    $self->element(
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                        {
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                            'Name' => 'Hsp_query-to',
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                %hitinfo = ();
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                last;
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            }
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            else {
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                $self->debug($_) if $verbose > 0;
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            }
 
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            # uncomment to see missed lines with verbose on
 
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            #else {
 
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            #    $self->debug($_);
 
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            #}
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        }
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        $last = $_;
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    }
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    # object begins so have to detect this in end_element for now
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    if ( $nm eq 'Hsp' ) {
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        foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq)) {
 
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            my $data = $self->{'_last_hspdata'}->{$_};
 
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            if ($data && $_ eq 'Hsp_hseq') {
 
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                # replace hmm '.' gap symbol by '-'
 
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                $data =~ s/\./-/g;
 
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            }
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            $self->element(
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                {
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                    'Name' => $_,
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                    'Data' => $self->{'_last_hspdata'}->{$_}
 
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                    'Data' => $data
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                }
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            );
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        }