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comparison miRDeep_plant.pl @ 46:ca05d68aca13 draft

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author big-tiandm
date Thu, 13 Nov 2014 22:43:35 -0500
parents 0c4e11018934
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45:2cb6add23dfe 46:ca05d68aca13
1 #!/usr/bin/perl 1 #!/usr/bin/perl
2 2
3 use warnings; 3 use warnings;
4 use strict; 4 use strict;
5 use Getopt::Std; 5 use Getopt::Std;
6 use RNA; 6 #use RNA;
7 7
8 8
9 ################################# MIRDEEP ################################################# 9 ################################# MIRDEEP #################################################
10 10
11 ################################## USAGE ################################################## 11 ################################## USAGE ##################################################
383 my $cpt_sup = 0; 383 my $cpt_sup = 0;
384 my $cpt_inf = 0; 384 my $cpt_inf = 0;
385 my $cpt_ega = 1; 385 my $cpt_ega = 1;
386 386
387 my ($seq,$number_of_randomizations)=@_; 387 my ($seq,$number_of_randomizations)=@_;
388 my $str =$seq; 388 #my $str =$seq;
389 my $mfe = RNA::fold($seq,$str); 389 #my $mfe = RNA::fold($seq,$str);
390 my $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`;
391 my @rawfolds=split/\s+/,$rnafold;
392 my $str=$rawfolds[1];
393 my $mfe=$rawfolds[-1];
394 $mfe=~s/\(//;
395 $mfe=~s/\)//;
390 396
391 for (my $i=0;$i<$number_of_randomizations;$i++) { 397 for (my $i=0;$i<$number_of_randomizations;$i++) {
392 $seq = shuffle_sequence_dinucleotide($seq); 398 $seq = shuffle_sequence_dinucleotide($seq);
393 $str = $seq; 399 #$str = $seq;
394 400
395 my $rand_mfe = RNA::fold($str,$str); 401 #my $rand_mfe = RNA::fold($str,$str);
402 $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`;
403 my @rawfolds=split/\s+/,$rnafold;
404 my $str=$rawfolds[1];
405 my $rand_mfe=$rawfolds[-1];
406 $rand_mfe=~s/\(//;
407 $rand_mfe=~s/\)//;
396 408
397 if ($rand_mfe < $mfe) { 409 if ($rand_mfe < $mfe) {
398 $cpt_inf++; 410 $cpt_inf++;
399 } 411 }
400 if ($rand_mfe == $mfe) { 412 if ($rand_mfe == $mfe) {