Given a sequence then separate the sequence to piece with certain overlap.

separate_seq.pl

#!/usr/bin/perl -w
use strict;
#use Data::Dumper;

# Usage:
# perl ./separate_seq.pl <piece length> <ovelap> <input file *.fa>

my ($l,$o,$f) = @ARGV;

open IN,"$f" || die $!;
$/ = ">"; <IN>; $/ = "\n";
while(<IN>){
	my $id = $1 if(/^(\S+)/);
	$/ = ">";
	my $seq = <IN>;
	chomp($seq);
	$/ = "\n";
	$seq =~ s/\n//g;
	my $total_len = length($seq);
	my $pos = 0;
	
	#print "total length: $total_len\n";
	for(my $i = 0; $i < $total_len; $i = $i + $l - 1){
		my $sub_seq;
		my $pos_old = $pos;
		#print $i,"\t";
		
		if($pos - $o < 0){
			if($pos + $l > $total_len){
				$sub_seq = substr($seq, $pos, $total_len - ($pos + 1) + 1);
				my $sub_len = $total_len - ($pos + 1) + 1;
				#print "$pos\t$sub_len\n";
			}else{
				$sub_seq = substr($seq, $pos, $l);
				#print "$pos\t$l\n";
			}
			$pos = $i + $l - $o;
		}else{
			if($pos + $l > $total_len){
				$sub_seq = substr($seq, $pos, $total_len - ($pos + 1) + 1);
				my $sub_len = $total_len - ($pos + 1) + 1;
				#print "$pos\t$sub_len\n";
			}else{
				$sub_seq = substr($seq, $pos - $o, $l);
				#print "$pos\t$l\n";
			}
			$pos = $i + $l - $o;
		}
		my $index_num = $pos_old+1;
		print ">",$id."_".$index_num,"\n",$sub_seq,"\n";
	}
	#print $id,"\n";
	#print $seq,"\n";
}
close IN;