PhD Student
Hello,
Im using a tool that produces for every barcode’s name a fastq file where every fastq file name contains the barcode number. I need to add the barcode number to all headers depending on their suitable barcodes. I used this command bellow but i need to apply this for all fastq and integrate it in my perl script:
perl -pe '$i = $i ? 0 : 1; s/^@/@BarcodeBC001--BC001_/ if $i' Run00213_BC001--BC001.fastq > Run00213_BC001--BC001_edit.fastq
With this command i could change the headers in all fastq files but i have to apply it one by one.
I need help if someone has an idea i would appreciate that.
Thank you in advance!
• 64 views
you mean something like this:
#!/usr/bin/perl
use strict;
use warnings;
open DIR, "/path/to/dir/" or die "cannot read directoryn";
while (my $file = readdir DIR) {
if ($file =~ /Rund+_(BCd+--BCd+).fastq/) {
my $barcode = $1;
my $new_file = $file;
$new_file =~ s/.fastq/_edit.fastq/;
warn "ediiting $file with barcode $barcode in $new_filen";
open (my $in, "<", $file) or die "cannot read $filen");
open (my $out, ">", $new_file) or die "cannot write $new_filen";
while (<$in>) {
s/^@/@Barcode$barcode_/;
print $out $_;
}
close $in;
close $out;
}
}
closedir DIR;
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