BOL: Perl script to split fasta sequence and create overlaps

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BioJoker
Perl script to split fasta sequence and create overlaps

Perl script to split fasta sequence and create overlaps

By BioJoker 2184 days ago

#!/usr/bin/perl

use strict;
use warnings;

my $len = 5000;
my $over = 200;
my $seq_id=$ARGV[0];
my $seqFile = $ARGV[1];
my $seq;

open(my $fh, "<", "$seqFile") or die "Can't open < $seqFile: $!";
while (<$fh>) {
    chomp;
    if (m/^>/) { $seq_id = $_; } else { $seq .= $_; }
}

for (my $i = 1; $i <= length $seq; $i += ($len - $over)) {
    my $s = substr ($seq, $i - 1, $len);
    print "$seq_id.($i-", $i + (length $s) - 1, ")\n$s\n";
}

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Perl script to split fasta sequence and create overlaps