CODEWITHSUNDEEP
perlbioinformaticsfastafastq
abraham
abraham

Reputation: 743

Convert multiples sequences from fastq to fasta in a folder

I want to convert all the fastq files contained in a folder to fasta format, each file will keep the original name but in fasta extension, I have made the next code in perl, however it only extract the last sequence of each file !!!

#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Long;

my ($dir, $files, $file_name, $file_format);

    GetOptions (
                'dr=s'  =>\$dir
                );

foreach $files (glob("$dir/*.fastq")) {
        open LINE, "<", $files or die "can't read open $files";
            while(
                    defined(my $head    = <LINE>)       &&
                    defined(my $seq     = <LINE>)       &&
                    defined(my $qhead   = <LINE>)       &&
                    defined(my $quality = <LINE>)           
            ){
                        substr($head, 0, 1, '>'); 
                        ($file_name, $file_format) = split (/\./,$files);
                        open OUTFILE, '>', $file_name.".fasta";
                        print OUTFILE $head, $seq;
            }
}
close LINE;
close OUTFILE;
exit;

and extra question, I want to use the pice next code, as a subroutine, I want to develop the same scrip to have the option of convert all fastq files in a folder or single file to fasta file !!!

while(
                        defined(my $head    = <LINE>)       &&
                        defined(my $seq     = <LINE>)       &&
                        defined(my $qhead   = <LINE>)       &&
                        defined(my $quality = <LINE>)           
                ){

Upvotes: 0

Views: 697

Answers (1)

FrankRalphBob
FrankRalphBob

Reputation: 434

Kinda of new to perl myself and don't know a thing about bioinformatics, but it looks like you are overwriting the output file with every turn of the while loop. I think you want to append to the file so you want a >> not just >. example

open OUTFILE, '>>', $file_name.".fasta";

Hope that helps.

Upvotes: 1

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