changeset 45:2cb6add23dfe draft

Deleted selected files

--- 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);	
-}
-