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Changeset 45:2cb6add23dfe (2014-10-30)

Previous changeset 44:0c4e11018934 (2014-10-30) Next changeset 46:ca05d68aca13 (2014-11-13)

Commit message:
Deleted selected files

removed:
randfold

diff -r 0c4e11018934 -r 2cb6add23dfe randfold
--- a/randfold Thu Oct 30 21:29:19 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,139 +0,0 @@
-# randfold (c) Eric Bonnet & Jan Wuyts 2003
-# randomization test for rna secondary structure
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
-
-# This soft needs BioPerl and ViennaRNA packages
-# See http://www.bioperl.org and http://www.tbi.univie.ac.at/~ivo/RNA/
-# See also README
-
-use strict;
-use Bio::SeqIO;
-use RNA;
-
-if (scalar(@ARGV) != 3) {
- die "Usage $0 fasta_file number_of_randomizations type[m|d]\n";
-}
-
-my $in = Bio::SeqIO->new(-file => "$ARGV[0]", -format => "fasta");
-my $number_of_randomizations = $ARGV[1];
-my $type = $ARGV[2];
-if ($type !~ /[m|d]/) {
- die "error: wrong type of randomization.";
-}
-
-while (my $o = $in->next_seq) {
- my $seq = uc($o->seq());
- my $name = $o->display_id();
-
- my $cpt_sup = 0;
- my $cpt_inf = 0;
- my $cpt_ega = 1;
-
- my $str = $seq;
- my $mfe = RNA::fold($seq,$str);
-
- for (my $i=0;$i<$number_of_randomizations;$i++) {
- if ($type eq "d") {
- $seq = shuffle_sequence_dinucleotide($seq);
- $str = $seq;
- }
- elsif ($type eq "m") {
- my @tmp = split //,$seq;
- fisher_yates_shuffle(\@tmp);
- $seq = join '',@tmp;
- $str = $seq;
- }
-
- my $rand_mfe = RNA::fold($str,$str);
-
- if ($rand_mfe < $mfe) {
- $cpt_inf++;
- }
- if ($rand_mfe == $mfe) {
- $cpt_ega++;
- }
- if ($rand_mfe > $mfe) {
- $cpt_sup++;
- }
- }
-
- my $proba = ($cpt_ega + $cpt_inf) / ($number_of_randomizations + 1);
-
- print "$name\t$mfe\t$proba\n";
-}
-
-# fisher_yates_shuffle( \@array ) :
-# generate a random permutation of @array in place
-# input array ref
-# return nothing
-sub fisher_yates_shuffle {
- my $array = shift;
- my $i;
- for ($i = @$array; --$i; ) {
- my $j = int rand ($i+1);
- next if $i == $j;
- @$array[$i,$j] = @$array[$j,$i];
- }
-}
-
-# shuffle a sequence while preserving dinucleotide distribution
-# input sequence string
-# return sequence string shuffled
-sub shuffle_sequence_dinucleotide {
-
- my ($str) = @_;
-
- # upper case and convert to ATGC
- $str = uc($str);
- $str =~ s/U/T/g;
-
- my @nuc = ('A','T','G','C');
- my $count_swap = 0;
- # set maximum number of permutations
- my $stop = length($str) * 10;
-
- while($count_swap < $stop) {
-
- my @pos;
-
- # look start and end letters
- my $firstnuc = $nuc[int(rand 4)];
- my $thirdnuc = $nuc[int(rand 4)];
-
- # get positions for matching nucleotides
- for (my $i=0;$i<(length($str)-2);$i++) {
- if ((substr($str,$i,1) eq $firstnuc) && (substr($str,$i+2,1) eq $thirdnuc)) {
- push (@pos,($i+1));
- $i++;
- }
- }
-
- # swap at random trinucleotides
- my $max = scalar(@pos);
- for (my $i=0;$i<$max;$i++) {
- my $swap = int(rand($max));
- if ((abs($pos[$swap] - $pos[$i]) >= 3) && (substr($str,$pos[$i],1) ne substr($str,$pos[$swap],1))) {
- $count_swap++;
- my $w1 = substr($str,$pos[$i],1);
- my $w2 = substr($str,$pos[$swap],1);
- substr($str,$pos[$i],1,$w2);
- substr($str,$pos[$swap],1,$w1);
- }
- }
- }
- return($str);
-}
-