#usr/local/bin/perl -w
use strict;
use Bio::SeqIO;

#headers format
#4	133005667	133005842

open(FILE,"/home/sakti/Desktop/trackseq_129S5_129S1/129S5ref_129S1qry_chr4_nonredundant") || die "cannot open file";

my $seqio = Bio::SeqIO->new(-file => "/home/sakti/Desktop/trackseq_129S5_129S1/135_155_129S5.fasta", -format => "fasta");

while(<FILE>){
	
	chomp($_);
	my @temp_data = split (/\s+/,$_);
	#Make name for the N files like 4_3000027_3020133.fsa
	my $name="4_".$temp_data[1]."_".$temp_data[2].".fasta";
	open (CORE,">$name");

	while(my $seq = $seqio->next_seq) {
  		print CORE $seq->subseq($temp_data[1],$temp_data[2]), "\n";
	}
	close(CORE);
}
close(FILE);