Perl script to extract a sequence from multifasta with range !

BioStar — Sat, 08 Sep 2018 09:55:49 -0500

# filterfastarange.pl
#!/usr/bin/perl
use strict;
use warnings;

#perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta

my $minlen = shift or die "Error: `minlen` parameter not provided\n";
my $maxlen = shift or die "Error: `maxlen` 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 and $seqlen <= maxlen);
    }
    local $/="\n";
}

BOL: Perl script to extract a sequence from multifasta with range !

Perl script to extract a sequence from multifasta with range !