Bio::Factory
EMBOSS
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Summary
Bio::Factory::EMBOSS - EMBOSS appliaction factory class
Package variables
No package variables defined.
Included modules
Bio::Tools::Run::EMBOSSApplication
Inherit
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
}
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->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 : _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 |
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 : 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 : $self->version
Usage : $embossfactory->version()
Function: gets the version of EMBOSS programs
Throws : if EMBOSS suite is not accessible
Returns : version value
Args : None |
Methods code
sub _program_list
{ my ($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);
$self->{'_groups'}->{$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 $1;
}
}
close(WOSSOUT);
}
1;} | sub location
{ my ($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 $self->{'_location'};} | sub new
{ my($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 $self; } | sub program
{ my ($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 $appl;} | sub program_info
{ my ($self, $value) = @_;
return $self->{'_programs'}->{$value};} | sub version
{ my ($self) = @_;
my ($version);
eval {
$version = `embossversion -auto`;
};
$self->throw("EMBOSS suite of programs is not available\n\n $@")
if $@;
chop $version;
my ($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;} | 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://bio.perl.org/MailList.html - About the mailing lists
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/
| AUTHOR - Heikki Lehvaslaiho | Top |
Email:
heikki@ebi.ac.ukAddress:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
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