Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Tools::Run::Genewise.3pm

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://bugzilla.open-bio.org/
 
 

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    :