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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://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, 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    :