Bio::Factory::EMBOSS(3pm) User Contributed Perl Documentation Bio::Factory::EMBOSS(3pm)
NAME
Bio::Factory::EMBOSS - EMBOSS application factory class
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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 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
perl v5.12.3 2011-06-18 Bio::Factory::EMBOSS(3pm)