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Viewing changes to Bio/SearchIO/hmmer_pull.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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Bio/SearchIO/hmmer_pull.pm
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# $Id: hmmer_pull.pm,v 1.1.2.4 2006/10/02 23:10:26 sendu Exp $
 
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# $Id: hmmer_pull.pm 11480 2007-06-14 14:16:21Z sendu $
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#
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# BioPerl module for Bio::SearchIO::hmmer_pull
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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_pull',
 
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    my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
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                               -file   => 't/data/hmmpfam.bigout');
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    while (my $result = $in->next_result) {
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        # this is a Bio::Search::Result::HmmpfamResult object
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=head2 new
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 Title   : new
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 Usage   : my $obj = new Bio::SearchIO::hmmer_pull();
 
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 Usage   : my $obj = Bio::SearchIO::hmmer_pull->new();
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 Function: Builds a new Bio::SearchIO::hmmer_pull object 
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 Returns : Bio::SearchIO::hmmer_pull
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 Args    : -fh/-file => HMMER output filename
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            my ($start, $end) = $self->_find_chunk_by_end("//\n");
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            return if $start == $end;
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            $self->_fields->{next_result} = new Bio::Search::Result::HmmpfamResult(-chunk => [($self->chunk, $start, $end)],
 
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            $self->_fields->{next_result} = Bio::Search::Result::HmmpfamResult->new(-chunk => [($self->chunk, $start, $end)],
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                                                                                   -parent => $self);
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            $self->{_end_of_previous_result} = $end;
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            # -piped_behaviour
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            my $chunk = $self->_get_chunk_by_end("//\n");
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            $chunk || return;
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            $self->_fields->{next_result} = new Bio::Search::Result::HmmpfamResult(-chunk => [$chunk],
 
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            $self->_fields->{next_result} = Bio::Search::Result::HmmpfamResult->new(-chunk => [$chunk],
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                                                                                   -parent => $self);
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        }
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    }