# BioPerl module for Bio::Tools::Run::Glimmer
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Bioperl
#
# Copyright Bioperl, Mark Johnson <mjohnson-at-watson-dot-wustl-dot-edu>
#
# 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::Glimmer - Wrapper for local execution of Glimmer,
GlimmerM and GlimmerHMM.
=head1 SYNOPSIS
# glimmer2
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmer3',
'-model' => 'model.icm');
# glimmer3
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmer2',
'-model' => 'model.icm');
# glimmerm
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmerm');
# glimmerHMM
my $factory =
Bio::Tools::Run::Glimmer->new('-program' => 'glimmerHMM');
# Pass the factory Bio::Seq objects
# returns a Bio::Tools::Glimmer object
my $glimmer = $factory->run($seq);
or
my $glimmer = $factor->run(@seq);
=head1 DESCRIPTION
Wrapper module for the Glimmer family of programs. Should work with
all currently available flavors: Glimmer, GlimmerM and GlimmerHMM.
However, only Glimmer 2.X and 3.X have been tested.
Glimmer is open source and available at
L<http://www.cbcb.umd.edu/software/glimmer/>.
GlimmerM is open source and available at
L<http://www.tigr.org/software/glimmerm/>.
GlimmerHMM is open source and available at
L<http://www.cbcb.umd.edu/software/GlimmerHMM/>.
Note that Glimmer 2.X 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).
Note that Glimmer 3.X produces two output files. This
module only passes the .predict file to Bio::Tools::Glimmer.
=head1 FEEDBACK
=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:
I<bioperl-l@bioperl.org>
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
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Mark Johnson
Email: mjohnson-at-watson-dot-wustl-dot-edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Glimmer;
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Glimmer;
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 model));
our @glimmer2_params = (qw(C L g i o p q s t w));
our @glimmer2_switches = (qw(M X f l r));
our @glimmer3_params = (qw(A C E L M P Z b g i t z));
our @glimmer3_switches = (qw(X f l o q r));
our @glimmerM_params = (qw(d g t));
our @glimmerM_switches = (qw(5 3 f r s));
our @glimmerHMM_params = (qw(d n p));
our @glimmerHMM_switches = (qw(f h v));
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: gets/sets the program name
Returns: string
Args : string
=cut
sub program_name {
my ($self, $val) = @_;
$self->program($val) if $val;
return $self->program();
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir()
Function: gets/sets the program dir
Returns: string
Args : string
=cut
sub program_dir {
my ($self, $val) = @_;
$self->{'_program_dir'} = $val if $val;
return $self->{'_program_dir'};
}
=head2 model
Title : model
Usage : $factory>model()
Function: gets/sets the name of the model (icm) file
Returns: string
Args : string
=cut
sub model {
my ($self, $val) = @_;
$self->{'_model'} = $val if $val;
return $self->{'_model'};
}
=head2 new
Title : new
Usage : $glimmer->new(@params)
Function: creates a new Glimmer factory
Returns: Bio::Tools::Run::Glimmer
Args :
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->io->_initialize_io();
$self->_set_from_args(
\@args,
-methods => [
@params,
@glimmer2_params,
@glimmer2_switches,
@glimmer3_params,
@glimmer3_switches,
@glimmerM_params,
@glimmerM_switches,
@glimmerHMM_params,
@glimmerHMM_switches
],
-create => 1,
);
unless (defined($self->program())) {
$self->throw('Must specify program');
}
unless (defined($self->model())) {
$self->throw('Must specify model');
}
return $self;
}
=head2 run
Title : run
Usage : $obj->run($seq_file)
Function: Runs Glimmer/GlimmerM/GlimmerHMM
Returns : A Bio::Tools::Glimmer object
Args : An array of Bio::PrimarySeqI objects
=cut
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);
my @run_args = ( $file_name );
# Glimmer 2.X ignores sequences after the first in a fasta file
# Glimmer 3.X will process multiple sequences at once
if ($program_name eq 'glimmer2') {
if (@seq > 1) {
$self->warn("Program $program_name processes one sequence at a time");
}
push @run_args, $seq[0]->display_id();
push @run_args, $seq[0]->length();
}
return $self->_run(@run_args);
}
=head2 _run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An instance of Bio::Tools::Glimmer
Args : file name, sequence identifier (optional)
=cut
sub _run {
my ($self, $seq_file_name, $seq_id, $seq_length) = @_;
my @cmd = (
$self->executable(),
$seq_file_name,
$self->model(),
split(/\s+/, $self->_setparams()),
);
my $cmd = join(' ', @cmd);
$self->debug("Glimmer Command = $cmd");
my $program_name = $self->program_name();
my ($output_fh, $output_file_name, $detail_file_name);
my ($program_stdout, $program_stderr);
my @ipc_args = (\@cmd, \undef);
# No STDOUT option for glimmer3, it takes a
# 'tag' argument, and outputs tag.predict and
# tag.detail. It seems that tag can be a path,
# which is handy.
if ($program_name eq 'glimmer3') {
my $temp_dir = $self->tempdir();
my $glimmer3_tag = "$temp_dir/glimmer3";
push @cmd, $glimmer3_tag;
$output_file_name = "$glimmer3_tag.predict";
$detail_file_name = "$glimmer3_tag.detail";
push @ipc_args, \$program_stdout, \$program_stderr;
}
else {
($output_fh, $output_file_name) = $self->io->tempfile(-dir=>$self->tempdir());
close($output_fh);
push @ipc_args, '>', $output_file_name;
push @ipc_args, '2>', \$program_stderr;
}
# 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.
eval {
IPC::Run::run(@ipc_args) || die $CHILD_ERROR;;
};
if ($EVAL_ERROR) {
$self->throw("Glimmer call crashed: $EVAL_ERROR");
}
$self->debug(join("\n", 'Glimmer STDOUT:', $program_stdout)) if $program_stdout;
$self->debug(join("\n", 'Glimmer STDERR:', $program_stderr)) if $program_stderr;
my %parser_args = (-file => $output_file_name);
# Pass along $seq_id and $seq_length if they were provided
# (only should be for glimmer2).
if (defined($seq_id)) { $parser_args{-seqname } = $seq_id; }
if (defined($seq_length)) { $parser_args{-seqlength} = $seq_length; }
# Pass along the name of extra output file, with handy information about
# sequence lengths (only produced by glimmer3)
if (defined($detail_file_name)) { $parser_args{-detail} = $detail_file_name; }
return Bio::Tools::Glimmer->new(%parser_args);
}
sub _setparams {
my ($self) = @_;
my $param_string = $self->SUPER::_setparams(
-params => [
@glimmer2_params,
@glimmer3_params,
@glimmerM_params,
@glimmerHMM_params,
],
-switches => [
@glimmer2_switches,
@glimmer2_switches,
@glimmerM_switches,
@glimmerHMM_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
=cut
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){
$out->write_seq($seq);
}
close($fh);
$out->close();
return $file_name;
}
1;