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.

FEEDBACK

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 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/

AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

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

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

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.

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

Internal methods

Do not call these methods directly

_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