Bio::Tools::Run::Genewise(3)

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 a Bio::SeqFeature::Gene::GeneStructure object
  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://bio.perl.org/MailList.html - 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.bioperl.org/

AUTHOR - FUGU Student Intern
Email: fugui@worf.fugu-sg.org

CONTRIBUTORS
Jason Stajich jason@bioperl.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, 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 $factory->run($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    :