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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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Bio/Tools/Match.pm
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package Bio::Tools::Match;
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use strict;
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use Bio::SeqFeature::Annotated;
 
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use Bio::SeqFeature::Generic;
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use Bio::Annotation::SimpleValue;
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use base qw(Bio::Root::Root Bio::Root::IO);
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    # Frequency of sites per nucleotide=32.347243
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    my ($matrix_id, $start, $strand, $core_score, $matrix_score, $seq) = $line =~ /^\s(\S+)\s+\|\s+(\d+)\s+\(([+-])\)\s+\|\s+(\S+)\s+\|\s+(\S+)\s+\|\s+(\S+)/;
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    my $feat = Bio::SeqFeature::Annotated->new(
 
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    my $feat = Bio::SeqFeature::Generic->new(
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        -seq_id => $self->{found_seq_id},
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        -start  => $start, 
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        -end    => $start + length($seq) - 1,