Mercurial > repos > big-tiandm > mirplant2
diff miRDeep_plant.pl @ 46:ca05d68aca13 draft
Uploaded
author | big-tiandm |
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date | Thu, 13 Nov 2014 22:43:35 -0500 |
parents | 0c4e11018934 |
children |
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--- a/miRDeep_plant.pl Thu Oct 30 21:29:35 2014 -0400 +++ b/miRDeep_plant.pl Thu Nov 13 22:43:35 2014 -0500 @@ -3,7 +3,7 @@ use warnings; use strict; use Getopt::Std; -use RNA; +#use RNA; ################################# MIRDEEP ################################################# @@ -385,14 +385,26 @@ my $cpt_ega = 1; my ($seq,$number_of_randomizations)=@_; - my $str =$seq; - my $mfe = RNA::fold($seq,$str); + #my $str =$seq; + #my $mfe = RNA::fold($seq,$str); + my $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`; + my @rawfolds=split/\s+/,$rnafold; + my $str=$rawfolds[1]; + my $mfe=$rawfolds[-1]; + $mfe=~s/\(//; + $mfe=~s/\)//; for (my $i=0;$i<$number_of_randomizations;$i++) { $seq = shuffle_sequence_dinucleotide($seq); - $str = $seq; + #$str = $seq; - my $rand_mfe = RNA::fold($str,$str); + #my $rand_mfe = RNA::fold($str,$str); + $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`; + my @rawfolds=split/\s+/,$rnafold; + my $str=$rawfolds[1]; + my $rand_mfe=$rawfolds[-1]; + $rand_mfe=~s/\(//; + $rand_mfe=~s/\)//; if ($rand_mfe < $mfe) { $cpt_inf++;