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

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@traviswheeler

This commit should properly be just a few lines of change to make_profile.pl to account for axis label changes, and to Profile.pm to account for handling of a new HMMER3/f file format that will eventually show its head in the HMMER 3.1 release. Sadly, things got tangled when I pulled changes from the upstream source (yours) after having already committed my changes ... so git apparently thinks a bunch of files have changed. I'm hopeful that on your end it doesn't look like as much change as it does on my end.

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Commits on Mar 22, 2012
  1. @traviswheeler

    Changing the axis labels in the make_profile.pl script

    traviswheeler authored
    Adding code to handle the HMMER3/f format (which will eventually see the light of
    day in H3.1 release)
  2. @traviswheeler
Commits on Sep 26, 2012
  1. @traviswheeler

    Merge branch 'master' of https://github.com/DaGaMs/Logomat

    traviswheeler authored
    Conflicts:
    	scripts/make_profile.pl
  2. @traviswheeler
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Showing with 11 additions and 9 deletions.
  1. +5 −3 HMM/Profile.pm
  2. +6 −6 scripts/make_profile.pl
View
8 HMM/Profile.pm
@@ -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) = $line =~ /^\s*(\d+)\s+(.*)\s+(\S+)\s+(\S)\s+(\S)\s+(\S)\s+(\S)\s*$/;
}
View
12 scripts/make_profile.pl
@@ -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;
@@ -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";
@@ -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";
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