#!/usr/bin/perl -w

use warnings;
use strict;
use diagnostics;

$/ = "//";
my $input = 'CUTR;AAABtest;plus;185-190;438-440;576-579';
  #two sets of "instructions" I can interchange in $input for testing
      #'CUTR25;AAAB01008851;plus;764935-764946;765050-765289;765372-765659'
      #'CUTR;AAABtest;plus;185-190;438-440;576-579'

	my @input = split (/;/, $input);
	my $name = $input[0];
	my $contig = $input[1];
	my $ori = $input[2];
	my @E1 = split (/-/, $input[3]);
	my @E2 = split (/-/, $input[4]);
	my @E3 = split (/-/, $input[5]);

print "$name\n$contig\n$ori\n@E1\n@E2\n@E3\n\n";

#get and edit contig so it can be searched and used
  my $contigfile = "$contig.txt";
  open(CONTIG, $contigfile) or die (">Could not open $contigfile!\n$!");
  my $rawseq = <CONTIG>;
  my $goodseq = editcontig($rawseq);


#clear giant variable to free some memory????
  $rawseq = '';

#Construct exon 1 and save to $EXON1
  my $offset1 = $E1[0]-1;

  my $length1 = $E1[1]-$offset1;

  my $EXON1 = '';
  $EXON1 = substr($goodseq, $offset1, $length1);

#Construct exon 2
  my $offset2 = $E2[0]-1;

  my $length2 = $E2[1]-$offset2;

  my $EXON2 = '';
  $EXON2 = substr($goodseq, $offset2, $length2);

#Construct exon3
  my $offset3 = $E3[0]-1;

  my $length3 = $E3[1]-$offset3;

  my $EXON3 = '';
  $EXON3 = substr($goodseq, $offset3, $length3);



print "$EXON1\n\n$EXON2\n\n$EXON3";

 exit;


 ########### SUBS ############

 sub editcontig {
  my ($rawseq) = @_;
  $rawseq =~ s/\s//g;
  $rawseq =~ s/0//g;
  $rawseq =~ s/1//g;
  $rawseq =~ s/2//g;
  $rawseq =~ s/3//g;
  $rawseq =~ s/4//g;
  $rawseq =~ s/5//g;
  $rawseq =~ s/6//g;
  $rawseq =~ s/7//g;
  $rawseq =~ s/8//g;
  $rawseq =~ s/9//g;
  return $rawseq;

}