annotate countDifferences.pl @ 0:a9fb5e4abb2d draft default tip

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#!/usr/bin/perl -w
use strict;
use warnings;
#use DateTime;
#use Date::Calc qw(:all);
use Bio::SeqIO;
#use String::Similarity;
#use StringOO::Similarity;
#use lib qw(./StringOO);
#use Similarity::similarity;

#use local::lib "$FindBin::Bin/..";  ### points to ~/mydir1 and local::lib finds lib
#use lib "$FindBin::StringOO/../lib";  
#package Similarity.pm;
#use String::Approx 'adistr';
#package String::Similarity;
#package String::Similarity qw(similarity);
#use String::Similarity;

##################################################################
## Perl program to count variants from aligned multi-FASTA file
##################################################################

my $file = $ARGV[0];
my %hSeq = ();
my @arrayID = ();
my $resultFile = $ARGV[1]; #"resultVariants.xls";
my $resultSimilarity = $ARGV[2]; #"resultSimilarity.xls";
my $chain = "";

	my $seqIO = Bio::SeqIO->new(-format=>'Fasta', -file=>$file);
			
	while (my $seq = $seqIO->next_seq()) {
		my $seqID = $seq->id;
		my $seqNuc = $seq->seq;
		push @arrayID, $seqID;
		$hSeq{$seqID} = $seqNuc;
		#my @seqArray = split //, $seqNuc;
	}
	
	open(RES, ">", $resultFile) or die "error open file $!:";
	open(SIM, ">", $resultSimilarity) or die "error open file $!:";
	
	print RES "\t";
	print SIM "\t";
	foreach my $id (@arrayID) {
		print RES "$id\t";
		print SIM "$id\t";
	}
	print RES "\n";
	print SIM "\n";
	
	for(my $i = 0; $i <= $#arrayID; $i++){
		print RES "$arrayID[$i]\t";
		print SIM "$arrayID[$i]\t";
		for(my $j = 0; $j <= $#arrayID; $j++){	#for(my $j = $i+1; $j <= $#arrayID; $j++){
			my $snpVariants = compare($hSeq{$arrayID[$i]}, $hSeq{$arrayID[$j]});
			#my $similarity = adistr($hSeq{$arrayID[$i]}, $hSeq{$arrayID[$j]});  
                        my $similarity = ident($hSeq{$arrayID[$i]}, $hSeq{$arrayID[$j]}); # replace similarity by ident
			my $roundSim = sprintf('%.3f', $similarity);
			print RES "$snpVariants\t";
			print SIM "$roundSim\t";
			#print RES ("SNPs between  $arrayID[$i] and $arrayID[$j] = $snpVariants\t");
		}
		print RES "\n";
		print SIM "\n";
	}

close(RES) or die "error when closing file $!:";
close(SIM) or die "error when closing file $!:";

	#foreach my $id (@arrayID) {
	#	my @seqArray = split //, $hSeq{$id};
	#	
	#}


#------------------------------------------------------------------------------	
# compare two aligned sequences
sub compare {
	my ($seq1,$seq2) = @_;
	#$seq1 = uc $seq1;
	#$seq2 = uc $seq2;
	my @seqArray1 = split //, $seq1;
	my @seqArray2 = split //, $seq2;
	my $variants = 0;
	
	for(my $i = 0; $i <= $#seqArray1; $i++){
		if( $seqArray1[$i] ne $seqArray2[$i] ){
			$variants++;
		}
	}
	
	return $variants;
}

# calculate percent identity between two aligned sequences
sub ident {
        my ($seq1,$seq2) = @_;
        #$seq1 = uc $seq1;
        #$seq2 = uc $seq2;
        my @seqArray1 = split //, $seq1;
        my @seqArray2 = split //, $seq2;
        my $sim = 0;

        for(my $i = 0; $i <= $#seqArray1; $i++){
                if( $seqArray1[$i] eq $seqArray2[$i] ){
                        $sim++;
                }
        }

        return ($sim / ($#seqArray1 + 1));
}

#------------------------------------------------------------------------------