annotate Perl/Naegleria/assignFastqByITS.pl @ 13:152d7c43478b draft default tip

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#!/usr/bin/perl

use strict;

my $directory;
if ($ARGV[0]){
	$directory = $ARGV[0];
}
else{
	print "You must provide as an argument a directory containing fastq.gz file for testing the presence of ITS sequences\nex: perl assignFastqByITS.pl my_fastq_dir\n";
	exit;
}

my %sequences =(
"1"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGCATCGA",
"2"=> "ATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
"3"=> "AAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
"4"=> "ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGCATCGA",
"5"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGCATCGA",
"6"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
"7"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
"8"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA"
);


open(LS,"ls $directory/*.fastq.gz |");
while(<LS>){
	my $file = $_;
	$file =~s/\n//g;$file =~s/\r//g;
	foreach my $genotype(sort {$a<=>$b} keys(%sequences)){
		my $seq = $sequences{$genotype};
		my $cmd = `zgrep -c '$seq' $file`;
		$cmd =~s/\n//g;$cmd =~s/\r//g;
		print "$file	$genotype	$cmd\n";
	}
}
close(LS);