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
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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)