BOL: Parse a Fasta file with Perl

BioScripts
Radha Agarkar
Parse a Fasta file with Perl

Parse a Fasta file with Perl

#!/usr/bin/env perl

# Usage:  fastaRead.pl data.fa

use strict;
use warnings;

my $filename = $ARGV[0];
my  $sequence;
open my $fileH, "<", $filename or die "could not open $filename\n";
while (<$fileH>) {
    chomp;
    if ($_ =~ /^>/) {
        print "this line is a header: $_\n";
    }
    else {
        print "this line contains sequence data: $_\n";
        # Concatenate everything from the file into a single var
        $sequence .= $_;
    }
}
close $fileH;

BOL

Radha Agarkar

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Parse a Fasta file with Perl