diff quantify.pl @ 46:ca05d68aca13 draft

Uploaded

--- a/quantify.pl	Thu Oct 30 21:29:35 2014 -0400
+++ b/quantify.pl	Thu Nov 13 22:43:35 2014 -0500
@@ -12,7 +12,7 @@
 use File::Basename;
 #use Getopt::Std;
 use Getopt::Long;
-use RNA;
+#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");
@@ -297,9 +297,17 @@
 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{$key});
+		#my ($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{$key}{"mfe"}=sprintf ("%.2f",$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);