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]
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include a thorough description of the problem with code and data examples if
at all possible.
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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 :