debian man page for bio::tools::run::embossapplication

Bio::Tools::Run::EMBOSSApplication(3pm) 		User Contributed Perl Documentation		   Bio::Tools::Run::EMBOSSApplication(3pm)

NAME
       Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications

SYNOPSIS
	 use Bio::Factory::EMBOSS;
	 # get an EMBOSS application object from the EMBOSS factory
	 $factory = Bio::Factory::EMBOSS->new();
	 $application = $factory->program('embossversion');
	 # run the application with an optional hash containing parameters
	 $result = $application->run(); # returns a string or creates a file
	 print $result . "
";

	 $water = $factory->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

	 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 = Bio::AlignIO->new(-format => 'emboss',
						     -file   => $wateroutfile);

	 while ( my $aln = $alnin->next_aln ) {
	     # process the alignment -- these will be Bio::SimpleAlign objects
	 }

DESCRIPTION
       The EMBOSSApplication class can represent EMBOSS any program. It is created by a Bio::Factory::EMBOSS object.

       If you want to check command line options before sending them to the program set $prog->verbose to positive integer. The ADC description of
       the available command line options is then parsed in and compared to input.

       See also Bio::Factory::EMBOSS 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

   CONTRIBUTORS
       Email: jason-AT-bioperl_DOT_org

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

   run
	Title	: run
	Usage	: $embossapplication->run($attribute_hash)
	Function: Runs the EMBOSS program.
	Returns : string or creates files for now; will return objects!
	Args	: hash of input to the program

   acd
	Title	: acd
	Usage	: $embossprogram->acd
	Function: finds out all the possible qualifiers for this
		  EMBOSS application. They can be used to debug the
		  options given.
	Throws	:
	Returns : boolean
	Args	:

   name
	Title	: name
	Usage	: $embossprogram->name
	Function: sets/gets the name of the EMBOSS program
		  Setting is done by the EMBOSSFactory object,
		  you should only get it.
	Throws	:
	Returns : name string
	Args	: None

   descr
	Title	: descr
	Usage	: $embossprogram->descr
	Function: sets/gets the descr of the EMBOSS program
		  Setting is done by the EMBOSSFactory object,
		  you should only get it.
	Throws	:
	Returns : description string
	Args	: None

   group
	Title	: group
	Usage	: $embossprogram->group
	Function: sets/gets the group of the EMBOSS program
		  Setting is done by the EMBOSSFactory object,
		  you should only get it.

		  If the application is assigned into a subgroup
		  use l<subgroup> to get it.
	Throws	:
	Returns : string, group name
	Args	: group string

   subgroup
	Title	: subgroup
	Usage	: $embossprogram->subgroup
	Function: sets/gets the subgroup of the EMBOSS program
		  Setting is done by the EMBOSSFactory object,
		  you should only get it.
	Throws	:
	Returns : string, subgroup name; undef if not defined
	Args	: None

   program_dir
	Title	: program_dir
	Usage	:
	Function: Required by WrapperBase
	Throws	:
	Returns : Name of directory with EMBOSS programs
	Args	:

   program_path
	Title	: program_path
	Usage	:
	Function: Required by WrapperBase
	Throws	:
	Returns : Full path of program
	Args	:

   executable
	Title	: executable
	Usage	:
	Function: Required by WrapperBase
	Throws	:
	Returns : Name of program
	Args	:

perl v5.12.3							    2011-06-18				   Bio::Tools::Run::EMBOSSApplication(3pm)