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

NAME

       Bio::Tools::Run::Pseudowise - Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence

SYNOPSIS

	 # Build a pseudowise alignment factory
	 my $factory = Bio::Tools::Run::Pseudowise->new();

	 # Pass the factory 3 Bio:SeqI objects (in the order of query
	 # peptide and cdna and target_genomic)
	 # @genes is an array of GenericSeqFeature objects
	 my @genes = $factory->run($seq1, $seq2, $seq3);

DESCRIPTION

       Pseudowise is a pseudogene predition program developed by Ewan Birney http://www.sanger.ac.uk/software/wise2.

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 one
       of 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 - Kiran
       Email kiran@fugu-sg.org

APPENDIX

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

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   version
	Title	: version
	Usage	: exit if $prog->version() < 1.8
	Function: Determine the version number of the program
	Example :
	Returns : float or undef
	Args	: none

   predict_genes
	Title	: predict_genes
	Usage	: DEPRECATED. Use $factory->run instead
	Function: Predict pseudogenes
	Returns : An array of Bio::Seqfeature::Generic objects
	Args	: Name of a file containing a set of 3 fasta sequences in the order of
		  peptide, cdna and genomic sequences
		  or else 3  Bio::Seq objects.

       Throws an exception if argument is not either a string (eg a filename) or 3 Bio::Seq objects.  If arguments are strings, throws exception
       if file corresponding to string name can not be found.

   run
	Title	: run
	Usage	: my @feats = $factory->run($seq1, $seq2, $seq3);
	Function: Executes pseudogene binary
	Returns : An array of Bio::Seqfeature::Generic objects
	Args	: Name of a file containing a set of 3 fasta sequences in the order of
		  peptide, cdna and genomic sequences
		  or else 3  Bio::Seq objects.

       Throws an exception if argument is not either a string (eg a filename) or 3 Bio::Seq objects.  If arguments are strings, throws exception
       if file corresponding to string name can not be found.

   _run
	Title	:  _run
	Usage	:  Internal function, not to be called directly
	Function:   makes actual system call to a pseudowise program
	Example :
	Returns : nothing; pseudowise  output is written to a
		  temporary file $TMPOUTFILE
	Args	: Name of a files containing 3 sequences in the order of peptide, cdna and genomic

   _parse_results
	Title	:  __parse_results
	Usage	:  Internal function, not to be called directly
	Function:  Parses pseudowise output
	Example :
	Returns : an reference to an array of Seqfeatures
	Args	: the name of the output file

   _setinput()
	Title	:  _setinput
	Usage	:  Internal function, not to be called directly
	Function:   Create input files for pseudowise program
	Example :
	Returns : name of file containing dba data input
	Args	: Seq objects in the order of query protein and cdna and target genomic sequence

   _query_pep_seq()
	Title	:  _query_pep_seq
	Usage	:  Internal function, not to be called directly
	Function:  get/set for the query sequence
	Example :
	Returns :
	Args	:

   _query_cdna_seq()
	Title	:  _query_cdna_seq
	Usage	:  Internal function, not to be called directly
	Function:  get/set for the query sequence
	Example :
	Returns :
	Args	:

   _subject_dna_seq()
	Title	:  _subject_dna_seq
	Usage	:  Internal function, not to be called directly
	Function:  get/set for the subject sequence
	Example :
	Returns :

	Args	:

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