package Index::EMBOSS;

use strict;
use warnings;
use Carp;

use POSIX qw(WIFEXITED WEXITSTATUS WIFSIGNALED WTERMSIG);
use IPC::Open3;

use base qw(Root);

use FASTA::File;

sub read_index { 1 }

sub get_sequence {
  my ( $self, $key ) = @_;
  croak "No value for get_sequence" unless $key;

  my @cmd = split / /, "seqret -filter $key";

  my $pid = open3( undef, \*RD, \*ERR, @cmd );

  my $seqs = FASTA::File->new( read => \*RD );
  my @err = <ERR>;

  pop @err;
  pop @err;

  close RD;
  close ERR;
  waitpid $pid, 0;

  # Everything was okay...
  if ( WIFEXITED($?) and not WEXITSTATUS($?) ) { return $seqs }

  # Non-zero exit
  elsif ( WIFEXITED($?) and WEXITSTATUS($?) ) {
    carp "seqret had a problem: $?; $!";
    carp @err;
  }

  # Was it stopped by an external program
  elsif ( WIFSIGNALED($?) ) {
    carp "seqret halted by external signal " . WTERMSIG($?);
  } else {
    carp "seqret suffered from a random pantwetting event";
  }

  return undef;
}

1;