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minor changes (axis labels, new HMMER3/f format) #3

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minor changes (axis labels, new HMMER3/f format) #3

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090a58f
Changing the axis labels in the make_profile.pl script
traviswheeler Mar 22, 2012
91dbb5d
Merge branch 'master' of https://github.com/DaGaMs/Logomat
traviswheeler Mar 22, 2012
c2172e9
Merge branch 'master' of https://github.com/DaGaMs/Logomat
traviswheeler Sep 26, 2012
7595139
Added FindBin module, to allow make_profile to be called from other d…
traviswheeler Sep 26, 2012
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8 changes: 5 additions & 3 deletions HMM/Profile.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -882,12 +882,14 @@ sub _parseFile3 {
# Match line
if ($substate == 0)
{
my ($s, $ascii, $map, $consensus, $rf, $cs);
my ($s, $ascii, $map, $consensus, $rf, $mm, $cs);

if ($self->version =~ /[abcd]$/) {
if ($self->version =~ /[abcd]$/) { # hmm versions a..d or greater
($s, $ascii, $map, $rf, $cs) = $line =~ /^\s*(\d+)\s+(.*)\s+(\S+)\s+(\S)\s+(\S)\s*$/;
} else { # hmm version e or greater
} elsif ($self->version =~ /e$/) { # hmm version e
($s, $ascii, $map, $consensus, $rf, $cs) = $line =~ /^\s*(\d+)\s+(.*)\s+(\S+)\s+(\S)\s+(\S)\s+(\S)\s*$/;
} else { # hmm version f or greater
($s, $ascii, $map, $consensus, $rf, $mm, $cs) = $line =~ /^\s*(\d+)\s+(.*)\s+(\S+)\s+(\S)\s+(\S)\s+(\S)\s+(\S)\s*$/;
}


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12 changes: 6 additions & 6 deletions scripts/make_profile.pl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
#!/usr/bin/env perl

use FindBin; # locate this script
use lib "$FindBin::Bin/.."; # use the parent directory; this is for HMM::Profile, calling from some other directory

use strict;
use warnings;
use HMM::Profile;
Expand All @@ -21,9 +24,6 @@
$logo->print_logo_dimensions(
-xsize => $xsize,
-ysize => $ysize,
-x_title => 'Relative Entropy',
-y_title => 'Contribution',
-graph_title => $graph_title,
-greyscale => $greyscale,
-height_logodds => $height_logodds
) or die "Error writing $outfile!\n";
Expand All @@ -35,13 +35,13 @@
-file => $outfile,
-xsize => $xsize,
-ysize => $ysize,
-x_title => 'Relative Entropy',
-y_title => 'Contribution',
-x_title => 'Position',
-y_title => 'Contribution (bits)',
-graph_title => $graph_title,
-greyscale => $greyscale,
-height_logodds => $height_logodds
) or die "Error writing $outfile!\n";

my $data = $logo->flatten($height_logodds);
#my $data = $logo->flatten($height_logodds);
#print STDOUT p( $data);
print STDOUT "Finished drawing Logo...\n";