Mercurial > repos > big-tiandm > mirplant2
diff precursors.pl @ 46:ca05d68aca13 draft
Uploaded
author | big-tiandm |
---|---|
date | Thu, 13 Nov 2014 22:43:35 -0500 |
parents | 4c0b1a94b882 |
children |
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--- a/precursors.pl Thu Oct 30 21:29:35 2014 -0400 +++ b/precursors.pl Thu Nov 13 22:43:35 2014 -0500 @@ -9,7 +9,7 @@ use strict; use Getopt::Long; -use RNA; +#use RNA; my %opts; GetOptions(\%opts,"map=s","g=s","d:i","f:i","o=s","e:f","s=s","h"); @@ -17,6 +17,7 @@ &usage; } +my $checkno=1; my $filein=$opts{'map'}; my $faout=$opts{'o'}; my $strout=$opts{'s'}; @@ -237,8 +238,14 @@ $tag2_end=$tag2_beg+length($tag2)-1; # fold - my ($struct,$mfe)=RNA::fold($seq); - $mfe=sprintf "%.2f", $mfe; + #my ($struct,$mfe)=RNA::fold($seq); + my $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`; + my @rawfolds=split/\s+/,$rnafold; + my $struct=$rawfolds[1]; + my $mfe=$rawfolds[-1]; + $mfe=~s/\(//; + $mfe=~s/\)//; + #$mfe=sprintf "%.2f", $mfe; if ($mfe > $MAX_ENERGY) {return 0;} # tag1 @@ -331,8 +338,14 @@ # fold - my ($struct,$mfe)=RNA::fold($seq); - $mfe=sprintf "%.2f",$mfe; + #my ($struct,$mfe)=RNA::fold($seq); + my $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`; + my @rawfolds=split/\s+/,$rnafold; + my $struct=$rawfolds[1]; + my $mfe=$rawfolds[-1]; + $mfe=~s/\(//; + $mfe=~s/\)//; + if ($mfe > $MAX_ENERGY) { $pass=0; return $pass;