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1 parent a0a4d0f commit e28267cfb7c1e3d3370e79cf2f1c312026157b42 @caballero committed May 7, 2012
Showing with 8 additions and 5 deletions.
  1. +8 −5 RepeatLandscape.pl
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@@ -70,6 +70,9 @@ =head1 LICENSE
my $html = undef;
my $opt = '';
+# PATH to required files
+my $dir = './';
+
# Calling options
GetOptions(
'h|help' => \$help,
@@ -96,20 +99,20 @@ =head1 LICENSE
if (defined $genome) {
warn "obtaining genome size from $genome\n" if (defined $verbose);
- system ("perl calcGenomeSize.pl $genome >> genome.size");
+ system ("perl $dir/calcGenomeSize.pl $genome >> genome.size");
}
warn "processing alignment file $align\n" if (defined $verbose);
-system ("perl KimuraDist_noCG_fromRMalign.pl -nolow $align > $sp.kout");
+system ("perl $dir/KimuraDist_noCG_fromRMalign.pl -nolow $align > $sp.kout");
warn "processing kimura file $sp.kout\n" if (defined $verbose);
$opt = '-v' if (defined $verbose);
-system ("perl parseKimuraOut.pl -k $sp.kout $opt");
+system ("perl $dir/parseKimuraOut.pl -g $dir/genome.size -k $sp.kout $opt");
warn "creating google chart using $sp.csv\n" if (defined $verbose);
if (defined $html) {
- system ("perl createGoogleVizHist.pl -c $sp.csv -t $name -o $sp.html");
+ system ("perl $dir/createGoogleVizHist.pl -c $sp.csv -p $dir/repeats.palette -t $name -o $sp.html");
}
else {
- system ("perl createGoogleVizHistJS.pl -c $sp.csv -t $name -o $sp.js");
+ system ("perl $dir/createGoogleVizHistJS.pl -c $sp.csv -p $dir/repeats.palette -t $name -o $sp.js");
}

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