Bio::Factory EMBOSS
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Summary
Bio::Factory::EMBOSS - EMBOSS application factory class
Package variables
No package variables defined.
Included modules
Bio::Factory::ApplicationFactoryI
Bio::Root::Root
Bio::Tools::Run::EMBOSSApplication
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
new
No description
Code
locationDescriptionCode
programDescriptionCode
versionDescriptionCode
program_infoDescriptionCode
_program_listDescriptionCode
Methods description
locationcode    nextTop
 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
programcodeprevnextTop
 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
versioncodeprevnextTop
 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
program_infocodeprevnextTop
 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
_program_listcodeprevnextTop
 Title   : _program_list
Usage : $embossfactory->_program_list()
Function: Finds out what programs are available.
Writes the names into an internal hash.
Returns : true if successful
Args : None
Methods code
newdescriptionprevnextTop
sub new {
  my($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 $self;
}
locationdescriptionprevnextTop
sub location {
    my ($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 $self->{'_location'};
}
programdescriptionprevnextTop
sub program {
    my ($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 $appl;
}
versiondescriptionprevnextTop
sub version {
    my ($self) = @_;
    my ($version);
    eval {
	$version = `embossversion -auto`;
    };
    $self->throw("EMBOSS suite of programs is not available\n\n $@")
	if $@;
    chop $version;

    # compare versions
$self->throw("EMBOSS has to be at least version $EMBOSSVERSION got $version\n") if $version lt $EMBOSSVERSION; return $version;
}
program_infodescriptionprevnextTop
sub program_info {
    my ($self, $value) = @_;
    return $self->{'_programs'}->{$value};
}
_program_listdescriptionprevnextTop
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);
	#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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
 
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.
Reporting BugsTop
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 LehvaslaihoTop
Email heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
ProgramsTop
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.
Internal methodsTop
Do not call these methods directly