Bio::Factory
EMBOSS
Toolbar
Summary
Bio::Factory::EMBOSS - EMBOSS application factory class
Package variables
No package variables defined.
Included modules
Bio::Factory::ApplicationFactoryI
Bio::Root::Root
Inherit
Bio::Factory::ApplicationFactoryI Bio::Root::Root
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 sequence against 1 or more 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({-sequences => $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
}
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 $prog->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
Bio::Tools::Run::EMBOSSApplication and
Bio::Tools::Run::EMBOSSacd.
Methods
Methods description
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 |
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 |
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 |
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 |
Title : _program_list
Usage : $embossfactory->_program_list()
Function: Finds out what programs are available.
Writes the names into an internal hash.
Returns : true if successful
Args : None |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my($location) =
$self->_rearrange([qw(LOCATION )],
@args);
$self->{ '_programs' } = {};
$self->{ '_programgroup' } = {};
$self->{ '_groups' } = {};
$self->location($location) if $location;
$self->_program_list;
return $self; } | sub location
{ my ($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 $self->{'_location'};} | sub program
{ my ($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 $appl;} | sub version
{ my ($self) = @_;
my ($version);
eval {
$version = `embossversion -auto`;
};
$self->throw("EMBOSS suite of programs is not available\n\n $@")
if $@;
chop $version;
$self->throw("EMBOSS has to be at least version $EMBOSSVERSION got $version\n")
if $version lt $EMBOSSVERSION;
return $version;} | sub program_info
{ my ($self, $value) = @_;
return $self->{'_programs'}->{$value};} | sub _program_list
{ my ($self) = @_;
if( $^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);
$self->{'_groups'}->{$groupname} = [] if $groupname;
while ( /^([a-z]\w+) +(.+)$/mg ) {
$self->{'_programs'}->{$1} = $2 if $1;
$self->{'_programgroup'}->{$1} = $groupname if $1;
push @{$self->{'_groups'}->{$groupname}}, $1 if $1;
}
}
close(WOSSOUT);
}
1;} | General documentation
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
Please direct usage questions or support issues to the mailing list:
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.
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://bugzilla.open-bio.org/
| AUTHOR - Heikki Lehvaslaiho | Top |
Email heikki-at-bioperl-dot-org
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
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.
Do not call these methods directly