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Bio::Factory::EMBOSS(3User Contributed Perl DocumentatiBio::Factory::EMBOSS(3)

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://bugzilla.open-bio.org/

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 v5.14.1			  2011-07-21	       Bio::Factory::EMBOSS(3)
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