/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Pseudowise

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

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 - 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, obtiained 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    :