BOL: Perl script to remove fasta sequences in multifasta file with certain length threshold

BioScripts
Poonam Mahapatra
Perl script to remove fasta sequences in multifasta file with certain length threshold

Perl script to remove fasta sequences in multifasta file with certain length threshold

By Poonam Mahapatra 2249 days ago

#!/usr/bin/perl
use strict;
use warnings;
 
my $minlen = shift or die "Error: `minlen` parameter not provided\n";
{
    local $/=">";
    while(<>) {
        chomp;
        next unless /\w/;
        s/>$//gs;
        my @chunk = split /\n/;
        my $header = shift @chunk;
        my $seqlen = length join "", @chunk;
        print ">$_" if($seqlen >= $minlen);
    }
    local $/="\n";
}