NAME

Bio::Tools::Run::Genewise - Object for predicting genes in a given sequence given a protein

SYNOPSIS

  # Build a Genewise alignment factory
  my $factory = Bio::Tools::Run::Genewise->new();

  # Pass the factory 2 Bio:SeqI objects (in the order of query peptide
  # and target_genomic).

  # @genes is an array of Bio::SeqFeature::Gene::GeneStructure objects
  my @genes = $factory->run($protein_seq, $genomic_seq);

  # Alternatively pass the factory a profile HMM filename and a
  # Bio:SeqI object (in the order of query HMM and target_genomic).

  # Set hmmer switch first to tell genewise to expect an HMM
  $factory->hmmer(1);
  my @genes = $factory->run($hmmfile, $genomic_seq);

DESCRIPTION

Genewise is a gene prediction program developed by Ewan Birney http://www.sanger.ac.uk/software/wise2.

Available Params:

NB: These should be passed without the '-' or they will be ignored, except switches such as 'hmmer' (which have no corresponding value) which should be set on the factory object using the AUTOLOADed methods of the same name.

  Model    [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
  Alg      [-kbyte,-alg]
  HMM      [-hmmer]
  Output   [-gff,-gener,-alb,-pal,-block,-divide]
  Standard [-help,-version,-silent,-quiet,-errorlog]

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 - FUGU Student Intern

Email: fugui@worf.fugu-sg.org

CONTRIBUTORS

Jason Stajich jason-AT-bioperl_DOT_org Keith James kdj@sanger.ac.uk

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 $factory->run($seq1,$seq2)
 Function: Predict genes
 Returns : A Bio::Seqfeature::Gene:GeneStructure object
 Args    : Name of a file containing a set of 2 fasta sequences in the order of
           peptide and genomic sequences
           or else 2  Bio::Seq objects.

Throws an exception if argument is not either a string (eg a filename) or 2 Bio::Seq objects. If arguments are strings, throws exception if file corresponding to string name can not be found.

run

 Title   : run
 Usage   : 2 sequence objects
           $genes = $factory->run($seq1, $seq2);
 Function: run
 Returns : A Bio::Seqfeature::Gene:GeneStructure object
 Args    : Names of a files each containing a fasta sequence in the order
           of either (peptide sequence, genomic sequence) or (profile HMM,
           genomic sequence). Alternatively any of the fasta sequence
           filenames may be substituted with a Bio::Seq object.

Throws an exception if argument is not either a string (eg a filename) or Bio::Seq objects. If arguments are strings, throws exception if file corresponding to string name can not be found. Also throws an exception if a profile HMM is expected (the -hmmer genewise switch has been set).

_run

 Title   : _run
 Usage   : Internal function, not to be called directly
 Function: Makes actual system call to a genewise program
 Example :
 Returns : L<Bio::SeqFeature::Gene::GeneStructure>
 Args    : Name of a files containing 2 sequences in the order of peptide and genomic

_setparams

 Title   :  _setparams
 Usage   :  Internal function, not to be called directly
 Function:  creates a string of params to be used in the command string
 Example :
 Returns :  string of params
 Args    :

_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    :

_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    :