# $Id$
#
# BioPerl module for Bio::Tools::Run::EMBOSSApplication
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications
=head1 SYNOPSIS
use Bio::Factory::EMBOSS;
# get an EMBOSS application object from the EMBOSS factory
$factory = Bio::Factory::EMBOSS->new();
$application = $factory->program('embossversion');
# run the application with an optional hash containing parameters
$result = $application->run(); # returns a string or creates a file
print $result . "\n";
$water = $factory->program('water');
# here is an example of running the application
# water can compare 1 seq against 1->many sequences
# in a database using Smith-Waterman
my $seq_to_test; # this would have a seq here
my @seqs_to_check; # this would be a list of seqs to compare
my $wateroutfile = 'out.water';
$water->run({-sequencea => $seq_to_test,
-seqall => \@seqs_to_check,
-gapopen => '10.0',
-gapextend => '0.5',
-outfile => $wateroutfile});
# now you might want to get the alignment
use Bio::AlignIO;
my $alnin = Bio::AlignIO->new(-format => 'emboss',
-file => $wateroutfile);
while ( my $aln = $alnin->next_aln ) {
# process the alignment -- these will be Bio::SimpleAlign objects
}
=head1 DESCRIPTION
The EMBOSSApplication class can represent EMBOSS any program. It is
created by a L<Bio::Factory::EMBOSS> object.
If you want to check command line options before sending them to the
program set $prog-E<gt>verbose to positive integer. The ADC
description of the available command line options is then parsed in
and compared to input.
See also L<Bio::Factory::EMBOSS> and L<Bio::Tools::Run::EMBOSSacd>.
=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 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 - Heikki Lehvaslaiho
Email heikki-at-bioperl-dot-org
=head2 CONTRIBUTORS
Email: jason-AT-bioperl_DOT_org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::EMBOSSApplication;
use vars qw( $SEQIOLOADED $ALIGNIOLOADED );
use strict;
use Data::Dumper;
use Bio::Tools::Run::EMBOSSacd;
use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
sub new {
my($class, $args) = @_;
my $self = $class->SUPER::new();
$self->name($args->{'name'});
$self->verbose($args->{'verbose'});
$self->acd if $self->verbose > 0;
return $self;
}
=head2 run
Title : run
Usage : $embossapplication->run($attribute_hash)
Function: Runs the EMBOSS program.
Returns : string or creates files for now; will return objects!
Args : hash of input to the program
=cut
sub run {
my ($self, $input) = @_;
$self->io->_io_cleanup();
# test input
$self->debug( Dumper($input) );
# parse ACD information
$self->acd if $self->verbose > 0;
# collect the options into a string
my $option_string = '';
foreach my $attr (keys %{$input}) {
my $attr_name = substr($attr, 1) if substr($attr, 0, 1) =~ /\W/;
my $array = 0;
if( defined $input->{$attr} && ref($input->{$attr}) ) {
my (@pieces);
if( $array = (ref($input->{$attr}) =~ /array/i) ) {
foreach my $s ( @{$input->{$attr}} ) {
@pieces = @{$input->{$attr}};
}
} else {
@pieces = ($input->{$attr});
}
if( ! defined $pieces[0] ) {
# we ignore for now
$self->warn("specified a parameter $attr with no value");
$input->{$attr} = undef;
return;
} elsif( $pieces[0]->isa('Bio::PrimarySeqI') ) {
unless( $SEQIOLOADED ) {
require Bio::SeqIO;
$SEQIOLOADED = 1;
}
my ($tfh,$tempfile) = $self->io->tempfile(-dir => $self->tempdir);
my $out = Bio::SeqIO->new(-format => 'fasta',
-fh => $tfh);
foreach my $seq ( @pieces ) {
$out->write_seq($seq);
}
$out->close();
$input->{$attr} = $tempfile;
close($tfh);
undef $tfh;
} elsif( $pieces[0]->isa('Bio::Align::AlignI') ) {
unless( $ALIGNIOLOADED ) {
require Bio::AlignIO;
$ALIGNIOLOADED = 1;
}
my ($tfh,$tempfile) = $self->io->tempfile();
my $out = Bio::AlignIO->new(-format => 'msf',
-fh => $tfh);
foreach my $p ( @pieces ) {
$out->write_aln($p);
}
$input->{$attr} = $tempfile;
close($tfh);
undef $tfh;
}
}
# check each argument against ACD
if ($self->verbose > 0) {
last unless defined $self->acd; # might not have the parser
$self->throw("Attribute [$attr] not recognized!\n")
unless $self->acd->qualifier($attr);
}
# print out debugging info
$self->debug("Input attr: ". $attr_name. " => ".
$input->{$attr}. "\n");
$option_string .= " " . $attr;
$option_string .= " ". $input->{$attr}
if defined $input->{$attr};
}
# check mandatory attributes against given ones
if ($self->verbose > 0) {
last unless defined $self->acd; # might not have the parser
# $self->acd->mandatory->print;
# if ($self->name eq 'water') {
# print Dumper($self->acd->mandatory);
# }
foreach my $attr (keys %{$self->acd->mandatory} ) {
last unless defined $self->acd; # might not have the parser
unless (defined $input->{$attr}) {
print "-" x 38, "\n", "MISSING MANDATORY ATTRIBUTE: $attr\n",
"-" x 38, "\n";
$self->acd->print($attr) and
$self->throw("Program ". $self->name.
" needs attribute [$attr]!\n")
}
}
}
my $runstring = join (' ', $self->name, $option_string, '-auto');
$self->debug( "Command line: ", $runstring, "\n");
return `$runstring`;
}
=head2 acd
Title : acd
Usage : $embossprogram->acd
Function: finds out all the possible qualifiers for this
EMBOSS application. They can be used to debug the
options given.
Throws :
Returns : boolean
Args :
=cut
sub acd {
my ($self) = @_;
unless ( $self->{'_acd'} ) {
$self->{'_acd'} =
Bio::Tools::Run::EMBOSSacd->new($self->name);
}
return $self->{'_acd'};
}
=head2 name
Title : name
Usage : $embossprogram->name
Function: sets/gets the name of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
Throws :
Returns : name string
Args : None
=cut
sub name {
my ($self,$value) = @_;
if (defined $value) {
$self->{'_name'} = $value;
}
return $self->{'_name'};
}
=head2 descr
Title : descr
Usage : $embossprogram->descr
Function: sets/gets the descr of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
Throws :
Returns : description string
Args : None
=cut
sub descr {
my ($self,$value) = @_;
if (defined $value) {
$self->{'_descr'} = $value;
}
return $self->{'_descr'};
}
=head2 group
Title : group
Usage : $embossprogram->group
Function: sets/gets the group of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
If the application is assigned into a subgroup
use l<subgroup> to get it.
Throws :
Returns : string, group name
Args : group string
=cut
sub group {
my ($self,$value) = @_;
if (defined $value) {
my ($group, $subgroup) = split ':', $value;
$self->{'_group'} = $group;
$self->{'_subgroup'} = $subgroup;
}
return $self->{'_group'};
}
=head2 subgroup
Title : subgroup
Usage : $embossprogram->subgroup
Function: sets/gets the subgroup of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
Throws :
Returns : string, subgroup name; undef if not defined
Args : None
=cut
sub subgroup {
my ($self) = @_;
return $self->{'_subgroup'};
}
=head2 program_dir
Title : program_dir
Usage :
Function: Required by WrapperBase
Throws :
Returns : Name of directory with EMBOSS programs
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{EMBOSS_ACDROOT});
}
=head2 program_path
Title : program_path
Usage :
Function: Required by WrapperBase
Throws :
Returns : Full path of program
Args :
=cut
sub program_path {
my $self = shift;
my $name = $self->{_name};
my $dir = Bio::Root::IO->catfile($ENV{EMBOSS_ACDROOT});
return "$dir/$name";
}
=head2 executable
Title : executable
Usage :
Function: Required by WrapperBase
Throws :
Returns : Name of program
Args :
=cut
sub executable {
my $self = shift;
$self->{_name};
}
1;