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bio::tools::run::pseudowise(3pm) [debian man page]

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)
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