#!/usr/bin/perl

# written for 410.633 into bioinformatics
# by erik

use strict;

use Bio::Tools::GuessSeqFormat;
use Bio::SeqIO;
use Bio::SeqFeature::Gene::Transcript;
use Bio::SeqFeature::Gene::Exon;

# USAGE: exonify <fil> "s1-e1,s2-e2,...sN-eN"
# returns the protein involved

my $fil = $ARGV[0];
my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$fil);
my $format  = $guesser->guess;
my $stream = Bio::SeqIO->new(-file => $fil,
                              -format => $format);

my $seq = $stream->next_seq();

die "Can't read seq" if !$seq;

my $exons=$ARGV[1];

my $f  = Bio::SeqFeature::Gene::Transcript->new();
my $stream = Bio::SeqIO->new(-fh =>\*STDOUT,
                              -format => "fasta");
for (split /,/, $exons) {
  my ($a,$b) = split(/-/,$_);
  my $ex = Bio::SeqFeature::Gene::Exon->new(-start=>$a,-end=>$b);

  $ex->is_coding(1);
  $ex->attach_seq($seq);
  #write each exon
  $stream->write_seq($ex->cds());
  $f->add_exon($ex);
}
$f->attach_seq($seq);

#write the mrna
$stream->write_seq($f->mrna());

#write the protein
$stream->write_seq($f->protein());