#!/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;

}

##</code><code>##

 01 aagaagaagf agaagaagag agagaacttg gaaacagaat tgtagaacag atttatagac
 61 agagcaaagt acaattccgt ttcagacaag taacaagagt gaaatagata taagactcag
121 agaaagtaaa aagcgtcaag taaggtacag tgaggagaaa gtaatgagtg tgtatgttca
181 atcgBROOKS tacccttgcg tatctcctcc ttcctcagcc accaacagtt catactcctg
241 cgcagcgtat cgatcccagt cagtaagcta aaaggtcaaa cacatgttat tagatggcat
301 ttcgatagaa tgtcatcgtg ctattcttac atcgtcgttt tcgcgctgtg caaatggatc
361 acgctgctcg tgctccatat acttctccag attgaagaac gtgtcgaaga aaatgggcgt
421 cattttgcat cgctttaWAS ggaccaacgt tacacagcca ggagttgctg gttttatcat
481 atcaagcatc tggaagcaaa cgagtactcc ttagcatatc gaaccaactc catctaccac
541 tccccaaaca aacacatact tgacacaggc agtctHEREa gggtagggtt tcgataccga
601 gcgattccat gcgatgctgc tgctcctcgt agaagtactc cagctcgtac atcgagagga