Permalink
Browse files

fixed spacing to 2 spaces

  • Loading branch information...
bretonics committed May 5, 2017
1 parent 5bb5df1 commit e538306f45fa693cc84f0f3d579710ac26f695db
Showing with 218 additions and 220 deletions.
  1. +33 −34 lib/SS.pm
  2. +185 −186 lib/Search.pm
@@ -24,22 +24,21 @@ use RNA; # ViennaRNA
=head1 NAME
SS - package for prediction and comparison of RNA secondary structures using ViennaRNA
SS - package for prediction and comparison of RNA secondary structures using ViennaRNA.
=head1 SYNOPSIS
Creation:
use SS;
use SS;
=head1 DESCRIPTION
This module is designed to predictic secondary structures of nucleotide sequences using ViennaRNA package
This module is designed to predictic secondary structures of nucleotide sequences using ViennaRNA package.
=head1 EXPORTS
=head2 Default Behaviors
Exports ss subroutine by default
Exports SS subroutine by default.
use SS;
@@ -52,58 +51,58 @@ use SS;
=head2 ss
Arg [1] : Name string
Arg [1] : Name string
Arg [2] : Sequence string
Arg [2] : Sequence string
Example : ss($name, $sequence)
Example : ss($name, $sequence)
Description : Predict secondary structures and output plots
Description : Predict secondary structures and output plots
Returntype : undef
Returntype : undef
Status : Stable
Status : Stable
=cut
sub ss {
my $filledUsage = 'Usage: ' . (caller(0))[3] . '($name, $sequence)';
@_ == 2 or confess wrongNumberArguments(), $filledUsage;
my $filledUsage = 'Usage: ' . (caller(0))[3] . '($name, $sequence)';
@_ == 2 or confess wrongNumberArguments(), $filledUsage;
my ($name, $sequence) = @_;
my $outFile = "$main::OUTDIR/ss/$name";
my $rnaPlot = "$outFile\_rna.ps";
my $dotPlot = "$outFile\_dot.ps";
my $rssPlot = "$outFile\_rss.ps";
my ($name, $sequence) = @_;
my $outFile = "$main::OUTDIR/ss/$name";
my $rnaPlot = "$outFile\_rna.ps";
my $dotPlot = "$outFile\_dot.ps";
my $rssPlot = "$outFile\_rss.ps";
my $F = RNA::pf_fold($sequence); # compute partition function and pair pobabilities
my ($ss, $mfe) = RNA::fold($sequence);
RNA::PS_rna_plot($sequence, $ss, $rnaPlot); # write PS plot to gRNA_#_rna.ps
RNA::PS_dot_plot($sequence, $dotPlot); # write dot plot to dot.ps
my $F = RNA::pf_fold($sequence); # compute partition function and pair pobabilities
my ($ss, $mfe) = RNA::fold($sequence);
RNA::PS_rna_plot($sequence, $ss, $rnaPlot); # write PS plot to gRNA_#_rna.ps
RNA::PS_dot_plot($sequence, $dotPlot); # write dot plot to dot.ps
my $command = "relplot.pl $rnaPlot $dotPlot > $rssPlot";
say "Running relative secondary structure command --> '$command'";
`$command`;
my $command = "relplot.pl $rnaPlot $dotPlot > $rssPlot";
say "Running relative secondary structure command --> '$command'";
`$command`;
return;
return;
}
=head1 COPYRIGHT AND LICENSE
Andres Breton (C)
Andres Breton (C)
[LICENSE]
[LICENSE]
=head1 CONTACT
=head1 CONTACT
Please email comments or questions to Andres Breton, me@andresbreton.com
Please email comments or questions to Andres Breton, dev@andresbreton.com
=head1 SETTING PATH
=head1 SETTING PATH
If PERL5LIB was not set, do something like this:
If PERL5LIB was not set, do something like this:
use FindBin; use lib "$FindBin::RealBin/lib";
use FindBin; use lib "$FindBin::RealBin/lib";
This finds and uses subdirectory 'lib' in current directoy as library location
This finds and uses subdirectory 'lib' in current directory as library location
=cut
Oops, something went wrong.

0 comments on commit e538306

Please sign in to comment.