Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer_workflow/Perl/Naegleria/assignFastqByITS.pl @ 1:032f6b3806a3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Thu, 30 May 2024 11:16:08 +0000
parents
children
comparison
equal deleted inserted replaced
0:3cbb01081cde 1:032f6b3806a3
1 #!/usr/bin/perl
2
3 use strict;
4
5 my $directory;
6 if ($ARGV[0]){
7 $directory = $ARGV[0];
8 }
9 else{
10 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";
11 exit;
12 }
13
14 my %sequences =(
15 "1"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGCATCGA",
16 "2"=> "ATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
17 "3"=> "AAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
18 "4"=> "ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGCATCGA",
19 "5"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGCATCGA",
20 "6"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
21 "7"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA",
22 "8"=>"ATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTTATGGTAAAAAAGGTGTATGGTAAAAAAGGTGAAAACCTTTTTTCCATTTACAAAAAATAACTCTGTGCAATGGAGCACACGGCTCGTGTATCGA"
23 );
24
25
26 open(LS,"ls $directory/*.fastq.gz |");
27 while(<LS>){
28 my $file = $_;
29 $file =~s/\n//g;$file =~s/\r//g;
30 foreach my $genotype(sort {$a<=>$b} keys(%sequences)){
31 my $seq = $sequences{$genotype};
32 my $cmd = `zgrep -c '$seq' $file`;
33 $cmd =~s/\n//g;$cmd =~s/\r//g;
34 print "$file $genotype $cmd\n";
35 }
36 }
37 close(LS);