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Viewing changes to Bio/DB/TFBS/transfac_pro.pm

  • 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/DB/TFBS/transfac_pro.pm
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    my $g_freq = ($seq =~ tr/g//) / length($seq);
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    my $t_freq = ($seq =~ tr/t//) / length($seq);
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    my $psm = new Bio::Matrix::PSM::SiteMatrix( -pA => $a,
 
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    my $psm = Bio::Matrix::PSM::SiteMatrix->new(-pA => $a,
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                                                -pC => $c,
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                                                -pG => $g,
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                                                -pT => $t,
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        #*** not always relative to gene start...
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        #    we need Bio::Map::Gene s to have some default tss and atg positions
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        #    that we can be relative to
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        my $rel = new Bio::Map::Relative(-element => $gene_map->gene, -description => $s_data[3]);
 
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        my $rel = Bio::Map::Relative->new(-element => $gene_map->gene, -description => $s_data[3]);
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        Bio::Map::Position->new(-map => $gene_map, -element => $tf, -start => $s_data[4], -end => $s_data[5], -relative => $rel);
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    }
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