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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Pseudowise 3pm"
.TH Bio::Tools::Run::Pseudowise 3pm "2018-09-14" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Pseudowise \- Object for prediting pseudogenes in a
given sequence given a protein and a cdna sequence
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  # 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);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Pseudowise is a pseudogene predition program developed by Ewan Birney
http://www.sanger.ac.uk/software/wise2.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Kiran"
.IX Header "AUTHOR - Kiran"
Email kiran@fugu\-sg.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS "version"
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : exit if $prog\->version() < 1.8
\& Function: Determine the version number of the program
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS "predict_genes"
.IX Subsection "predict_genes"
.Vb 7
\& 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.
.Ve
.PP
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.
.SS "run"
.IX Subsection "run"
.Vb 7
\& 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.
.Ve
.PP
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.
.SS "_run"
.IX Subsection "_run"
.Vb 7
\& 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
.Ve
.SS "_parse_results"
.IX Subsection "_parse_results"
.Vb 6
\& 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
.Ve
.SS "\fI_setinput()\fP"
.IX Subsection "_setinput()"
.Vb 6
\& 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
.Ve
.SS "\fI_query_pep_seq()\fP"
.IX Subsection "_query_pep_seq()"
.Vb 6
\& Title   :  _query_pep_seq
\& Usage   :  Internal function, not to be called directly
\& Function:  get/set for the query sequence 
\& Example :
\& Returns : 
\& Args    :
.Ve
.SS "\fI_query_cdna_seq()\fP"
.IX Subsection "_query_cdna_seq()"
.Vb 6
\& Title   :  _query_cdna_seq
\& Usage   :  Internal function, not to be called directly
\& Function:  get/set for the query sequence
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "\fI_subject_dna_seq()\fP"
.IX Subsection "_subject_dna_seq()"
.Vb 5
\& Title   :  _subject_dna_seq
\& Usage   :  Internal function, not to be called directly
\& Function:  get/set for the subject sequence
\& Example :
\& Returns :
\&
\& Args    :
.Ve