Raw content of Bio::Factory::EMBOSS
<![CDATA[# $Id: EMBOSS.pm,v 1.10 2002/10/22 07:38:32 lapp Exp $
#
# BioPerl module for Bio::Factory::EMBOSS
#
#
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
#
# 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::Factory::EMBOSS - EMBOSS appliaction factory class
=head1 SYNOPSIS
# get an EMBOSS factory
use Bio::Factory::EMBOSS;
$f = Bio::Factory::EMBOSS -> new();
# get an EMBOSS application object from the factory
$water = $f->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
# (could be just 1)
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 = new Bio::AlignIO(-format => 'emboss',
-file => $wateroutfile);
while( my $aln = $alnin->next_aln ) {
# process the alignment -- these will be Bio::SimpleAlign objects
}
=head1 DESCRIPTION
The EMBOSS factory class encapsulates access to EMBOSS programs. A
factory object allows creation of only known applications.
If you want to check command line options before sending them to the
program set $factory-E<gt>verbose to positive integer. The value is
passed on to programs objects and the ADC description of the available
command line options is parsed and compared to input.
See also L<Bio::Tools::Run::EMBOSSApplication> 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://bio.perl.org/MailList.html - About the mailing lists
=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
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=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::Factory::EMBOSS;
use vars qw(@ISA $EMBOSSVERSION);
use strict;
use Bio::Root::Root;
use Bio::Tools::Run::EMBOSSApplication;
use Bio::Factory::ApplicationFactoryI;
@ISA = qw(Bio::Root::Root Bio::Factory::ApplicationFactoryI );
$EMBOSSVERSION = "2.0.0";
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
# set up defaults
my($location) =
$self->_rearrange([qw(LOCATION )],
@args);
$self->{ '_programs' } = {};
$self->{ '_programgroup' } = {};
$self->{ '_groups' } = {};
$self->location($location) if $location;
$self->_program_list; # retrieve info about available programs
return $self;
}
=head2 location
Title : location
Usage : $embossfactory->location
Function: get/set the location of EMBOSS programs.
Valid values are 'local' and 'novella'.
Returns : string, defaults to 'local'
Args : string
=cut
sub location {
my ($self, $value) = @_;
my %location = ('local' => '1',
'novella' => '1'
);
if (defined $value) {
$value = lc $value;
if ($location{$value}) {
$self->{'_location'} = $value;
} else {
$self->warn("Value [$value] not a valid value for ".
"location(). Defaulting to [local]");
$self->{'_location'} = 'local';
}
}
$self->{'_location'} ||= 'local';
return $self->{'_location'};
}
=head2 program
Title : program
Usage : $embossfactory->program('program_name')
Function: Creates a representation of a single EMBOSS program
Returns : Bio::Tools::Run::EMBOSSApplication object
Args : string, program name
=cut
sub program {
my ($self, $value) = @_;
unless( $self->{'_programs'}->{$value} ) {
$self->warn("Application [$value] is not available!");
return undef;
}
my $attr = {};
$attr->{name} = $value;
$attr->{verbose} = $self->verbose;
my $appl = Bio::Tools::Run::EMBOSSApplication ->new($attr);
return $appl;
}
=head2 version
Title : $self->version
Usage : $embossfactory->version()
Function: gets the version of EMBOSS programs
Throws : if EMBOSS suite is not accessible
Returns : version value
Args : None
=cut
sub version {
my ($self) = @_;
my ($version);
eval {
$version = `embossversion -auto`;
};
$self->throw("EMBOSS suite of programs is not available \n\n$@")
if $@;
chop $version;
# compare versions
my ($thisv, $embossv);
$version =~ /(\d+)\.(\d+)\.(\d+)/;
$thisv = "$1.$2$3";
$EMBOSSVERSION =~ /(\d+)\.(\d+)\.(\d+)/;
$embossv = "$1.$2$3";
$self->throw("EMBOSS has to be at least version $EMBOSSVERSION\n")
if $thisv < $embossv;
return $version;
}
=head2 Programs
These methods allow the programmer to query the EMBOSS suite and find
out which program names can be used and what arguments can be used.
=head2 program_info
Title : program_info
Usage : $embossfactory->program_info('emma')
Function: Finds out if the program is available.
Returns : definition string of the program, undef if program name not known
Args : string, prgramname
=cut
sub program_info {
my ($self, $value) = @_;
return $self->{'_programs'}->{$value};
}
=head2 Internal methods
Do not call these methods directly
=head2 _program_list
Title : _program_list
Usage : $embossfactory->_program_list()
Function: Finds out what programs are available.
Writes the names into an internal hash.
Returns : true if successful
Args : None
=cut
sub _program_list {
my ($self) = @_;
if( $^O =~ /MSWIN/i ||
$^O =~ /Mac/i ) { return; }
{
local * SAVERR;
open SAVERR, ">&STDERR";
open STDERR, ">/dev/null";
open(WOSSOUT, "wossname -auto |") || return;
open STDERR, ">&SAVERR";
}
local $/ = "\n\n";
while(<WOSSOUT> ) {
my ($groupname) = (/^([A-Z][A-Z0-9 ]+)$/m);
#print $groupname, "\n" if $groupname;
$self->{'_groups'}->{$groupname} = [] if $groupname;
while ( /^([a-z]\w+) +(.+)$/mg ) {
#print "$1\t$2 \n" if $1;
$self->{'_programs'}->{$1} = $2 if $1;
$self->{'_programgroup'}->{$1} = $groupname if $1;
push @{$self->{'_groups'}->{$groupname}}, $1 if $1;
}
}
close(WOSSOUT);
}
1;
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