comparison quantify.pl @ 46:ca05d68aca13 draft

Uploaded

45:2cb6add23dfe

use File::Path;
use strict;
use File::Basename;
#use Getopt::Std;
use Getopt::Long;
use RNA;

my %opts;
GetOptions(\%opts,"r=s","p=s","m=s","mis:i","t:i","e:i","f:i","tag:s","o=s","time:s","h");
if (!(defined $opts{r} and defined $opts{p} and defined $opts{m} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;

}

sub structure{
	foreach my $key (keys %pre_mature) {
		if (!(defined $pre{$key})){die "!!!!! No precursor sequence $key, please check it!\n";}
		my ($str,$mfe)=RNA::fold($pre{$key});
		$struc{$key}{"struc"}=$str;
		$struc{$key}{"mfe"}=sprintf ("%.2f",$mfe);

		foreach my $id (keys %{$pre_mature{$key}}) {
			($pre_mature{$key}{$id}{"star"}[0],$pre_mature{$key}{$id}{"star"}[1])=&other_pair($pre_mature{$key}{$id}{"mature"}[0],$pre_mature{$key}{$id}{"mature"}[1],$str);
		}
=cut

46:ca05d68aca13

use File::Path;
use strict;
use File::Basename;
#use Getopt::Std;
use Getopt::Long;
#use RNA;

my %opts;
GetOptions(\%opts,"r=s","p=s","m=s","mis:i","t:i","e:i","f:i","tag:s","o=s","time:s","h");
if (!(defined $opts{r} and defined $opts{p} and defined $opts{m} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;

}

sub structure{
	foreach my $key (keys %pre_mature) {
		if (!(defined $pre{$key})){die "!!!!! No precursor sequence $key, please check it!\n";}
		#my ($str,$mfe)=RNA::fold($pre{$key});
		my $rnafold=`perl -e 'print "$pre{$key}"' | RNAfold --noPS`;
		my @rnafolds=split/\s+/,$rnafold;
		my $str=$rnafolds[1];
		my $mfe=$rnafolds[-1];
		$mfe=~s/\(//;
		$mfe=~s/\)//;

		$struc{$key}{"struc"}=$str;
		#$struc{$key}{"mfe"}=sprintf ("%.2f",$mfe);
		$struc{$key}{"mfe"}=$mfe;

		foreach my $id (keys %{$pre_mature{$key}}) {
			($pre_mature{$key}{$id}{"star"}[0],$pre_mature{$key}{$id}{"star"}[1])=&other_pair($pre_mature{$key}{$id}{"mature"}[0],$pre_mature{$key}{$id}{"mature"}[1],$str);
		}
=cut