# BioPerl module for Bio::Tools::Run::Genemark
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
# Cared for by Bioperl
# Copyright Bioperl, Mark Johnson <johnsonm-at-gmail-dot-com>
# Special thanks to Chris Fields, Sendu Bala
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Genemark - Wrapper for local execution of the GeneMark
family of programs.


  # GeneMark.hmm (prokaryotic)
  my $factory =
      Bio::Tools::Run::Genemark->new('-program' => 'gmhmmp',
                                     '-m'       => 'model.icm');

  # Pass the factory Bio::Seq objects
  # returns a Bio::Tools::Genemark object
  my $genemark = $factory->run($seq);


Wrapper module for the GeneMark family of programs.  Should work with
all flavors of GeneMark.hmm at least, although only the prokaryotic
version has been tested.

General information about GeneMark is available at

Contact information for licensing inquiries is available at:

Note that GeneMark.hmm (prokaryotic at least)  will only process the
first sequence in a fasta file (if you run() more than one sequence
at a time, only the first will be processed).


=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:


rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the


=head1 AUTHOR - Mark Johnson 

 Email: johnsonm-at-gmail-dot-com


The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _


package Bio::Tools::Run::Genemark;

use strict;
use warnings;

use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Genemark;
use English;
use IPC::Run;     # Should be okay on WIN32 (See IPC::Run Docs)

use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);

our @params            = (qw(program));
our @genemark_params   = (qw(i m p));
our @genemark_switches = (qw(a n r));

=head2 program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: gets/sets the program name
 Returns:  string
 Args    : string


sub program_name {
    my ($self, $val) = @_;
    $self->program($val) if $val;
    return $self->program();


=head2 program_dir

 Title   : program_dir
 Usage   : $factory->program_dir()
 Function: gets/sets the program dir
 Returns:  string
 Args    : string


sub program_dir {
    my ($self, $val) = @_;
    $self->{'_program_dir'} = $val if $val;
    return $self->{'_program_dir'};

=head2 new

 Title   : new
 Usage   : $genemark->new(@params)
 Function: creates a new Genemark factory
 Returns:  Bio::Tools::Run::Genemark
 Args    : 


sub new {
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args);
                             -methods => [
                             -create  => 1,
       unless (defined($self->program())) {
           $self->throw('Must specify program');
       unless (defined($self->m())) {
           $self->throw('Must specify model');
       return $self;

=head2 run

 Title   :   run
 Usage   :   $obj->run($seq_file)
 Function:   Runs Genemark
 Returns :   A Bio::Tools::Genemark object
 Args    :   An array of Bio::PrimarySeqI objects


sub run {
    my ($self, @seq) = @_;

    unless (@seq) {
        $self->throw("Must supply at least one Bio::PrimarySeqI");
    foreach my $seq (@seq) {
        unless ($seq->isa('Bio::PrimarySeqI')) {
            $self->throw("Object does not implement Bio::PrimarySeqI");

    my $program_name = $self->program_name();
    my $file_name    = $self->_write_seq_file(@seq);

    # GeneMark.hmm (prokaryotic version, anyway) ignores sequences after the
    # first in a fasta file
    if ($program_name eq 'gmhmmp') {
        if (@seq > 1) {
            $self->warn("Program $program_name processes one sequence at a time");
    return $self->_run($file_name, $seq[0]->display_id());

=head2 _run

 Title   :   _run
 Usage   :   $obj->_run()
 Function:   Internal(not to be used directly)
 Returns :   An instance of Bio::Tools::Genemark 
 Args    :   file name, sequence identifier (optional)


sub _run {
    my ($self, $seq_file_name, $seq_id) = @_;

    my ($temp_fh, $temp_file_name) =

    # IPC::Run wants an array where the first element is the executable
    my @cmd = (
               split(/\s+/, $self->_setparams()),

    my $cmd = join(' ', @cmd);
    $self->debug("GeneMark Command = $cmd");

    # Run the program via IPC::Run so:
    # 1) The console doesn't get cluttered up with the program's STDERR/STDOUT
    # 2) We don't have to embed STDERR/STDOUT redirection in $cmd
    # 3) We don't have to deal with signal handling (IPC::Run should take care
    #    of everything automagically. 
    my ($program_stdout, $program_stderr);
    eval {
                  ) || die $CHILD_ERROR;
    if ($EVAL_ERROR) {
        $self->throw("GeneMark call crashed: $EVAL_ERROR"); 

    ## The prokaryotic version of GeneMark.HMM, at least, returns
    ## 0 (success) even when the license has expired.   
    if ((-z $temp_file_name) && ($program_stderr =~ /license period has ended/i)) {
    elsif ($program_stderr =~ /\d+ days remaining/i) {

    $self->debug(join("\n", 'GeneMark STDOUT:', $program_stdout)) if $program_stdout;
    $self->debug(join("\n", 'GeneMark STDERR:', $program_stderr)) if $program_stderr;
    return Bio::Tools::Genemark->new(-file    => $temp_file_name,
                                     -seqname => $seq_id);

sub _setparams {
    my ($self) = @_;
    my $param_string = $self->SUPER::_setparams(
                                                -params   => [@genemark_params],
                                                -switches => [@genemark_switches],
                                                -dash     => 1,

    # Kill leading and trailing whitespace
    $param_string =~ s/^\s+//g;
    $param_string =~ s/\s+$//g;

    return $param_string;

=head2 _write_seq_file

 Title   :   _write_seq_file
 Usage   :   obj->_write_seq_file($seq) or obj->_write_seq_file(@seq)
 Function:   Internal(not to be used directly)
 Returns :   Name of a temp file containing program output
 Args    :   One or more Bio::PrimarySeqI objects


sub _write_seq_file {

    my ($self, @seq) = @_;
    my ($fh, $file_name) = $self->io->tempfile(-dir=>$self->tempdir());
    my $out              = Bio::SeqIO->new(-fh => $fh , '-format' => 'Fasta');

    foreach my $seq (@seq){

    return $file_name;