| Bio::Tools::Run::Genewise(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Genewise(3pm) |
Bio::Tools::Run::Genewise - Object for predicting genes in a given sequence given a protein
# 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);
Genewise is a gene prediction program developed by Ewan Birney http://www.sanger.ac.uk/software/wise2.
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]
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
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.
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/
Email: fugui@worf.fugu-sg.org
Jason Stajich jason-AT-bioperl_DOT_org Keith James kdj@sanger.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none
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.
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).
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
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 :
Title : _query_pep_seq Usage : Internal function, not to be called directly Function: get/set for the query sequence Example : Returns : Args :
Title : _subject_dna_seq Usage : Internal function, not to be called directly Function: get/set for the subject sequence Example : Returns : Args :
| 2021-01-06 | perl v5.32.0 |