Summary

G::Seq::FreeEnergy - Perl extension for blah blah blah

Package variables

Included modules

Inherit

AutoLoader Exporter

Synopsis

  use G::Seq::FreeEnergy;
  blah blah blah

Description

Stub documentation for G::Seq::FreeEnergy was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.
Blah blah blah.

Methods

Methods description

None available.

Methods code

sub DESTROY {

    my $self = shift;

}

sub RNAfold {

    &opt_default(output=>"stdout",filename=>'FreeEnergy.csv');
    my @args=opt_get(@_);

    my $seq=shift @args;
    my $start=shift @args;
    my $end=shift @args;
    my $filename=opt_val("filename");
    my $rna_fold_result;
    my $sq;
    my $num;
    my $result;

    $sq = substr($seq,$start,$end-$start + 1);
    $rna_fold_result=qx!echo $sq | RNAfold!;
    $num++;
#    $result=(split(/\s\(\s/,$rna_fold_result))[1];
#    $result=~tr/\)\n//d;
# unable to retrive sequence over 58 letters
# suggested by Atsuko Kisi and Hayataro Kouchi

    $result = (split(/\(/, $rna_fold_result))[-1];
    chomp($result);
    $result =~ s/\)//;

    if(&opt_val("output") eq "stdout"){
	&msg_send($result,"\n");
    }
    if(&opt_val("output") eq "f"){
	open(FILE,">>$filename");
	print FILE $result,"\n";
	close(FILE);
    }
    
    mkdir("graph",0777);
    system('mv','rna.ps','graph/');

    return $result;

}

sub foreach_RNAfold {

    &opt_default(window=>50,output=>"show",filename=>"FreeEnergy.csv");
    my @args=opt_get(@_);
    
    my $seq=shift @args;
    my $start=shift @args;
    my $end=shift @args;
    my $number=opt_val("window");
    my $printer=opt_val("output");
    my $filename=opt_val("filename");
    my $i;
    my $cut;
    my $array;
    my $rna_fold_result;
    my $sq;
    my $num;
    my $x;
    my $y;
    my @y;
    my @RNA;


    if($printer=~/f/){
	open(FILE,">$filename");
    }

    $cut = substr($$seq,$start,$end-$start);


    for($i=0 ; $i<=length($cut)-$number ; $i=$i+1){
 
        $y=$i+$start;
        $sq = substr($$seq,$y,$number);


        $rna_fold_result=qx!echo $sq | RNAfold!;
        $num++;
        $rna_fold_result=~tr/()//d;
        $rna_fold_result=~tr/[A-Z]\n//d;
        $rna_fold_result=~s/\.\.//g;
        $rna_fold_result=~s/\.\ //g;
	$rna_fold_result=~tr/ //d;
	push(@RNA,$rna_fold_result);

	if($printer=~/f/){
	    print FILE $y,",",$y+$number,",",$rna_fold_result,"\n";
	}
	if($printer!~/[fn]/){
	    &msg_send($y,"..",$y+$number,"\t",$rna_fold_result,"\n");
 	}
	push(@y,$y);
    }
    
    unlink("rna.ps");

    if($printer=~/g/ || $printer=~/show/){
        &G::Tools::Graph::_UniMultiGrapher(\@y,\@RNA,-filename=>"FreeEnergy.png",-x=>"position",-y=>"free energy",-title=>"free energy");
    }

    msg_gimv('graph/FreeEnergy.png') if($printer=~/show/);

    return\@ RNA;

}

General documentation

A. U. Thor, a.u.thor@a.galaxy.far.far.away

perl(1).