1Bio::Tools::Run::GenewiUssee(r3)Contributed Perl DocumenBtiaot:i:oTnools::Run::Genewise(3)
2
6 Bio::Tools::Run::Genewise - Object for predicting genes in a given
7 sequence given a protein
8
10 # Build a Genewise alignment factory
11 my $factory = Bio::Tools::Run::Genewise->new();
12 # Pass the factory 2 Bio:SeqI objects (in the order of query peptide
14 # and target_genomic).
15 # @genes is an array of Bio::SeqFeature::Gene::GeneStructure objects
17 my @genes = $factory->run($protein_seq, $genomic_seq);
18 # Alternatively pass the factory a profile HMM filename and a
20 # Bio:SeqI object (in the order of query HMM and target_genomic).
21 # Set hmmer switch first to tell genewise to expect an HMM
23 $factory->hmmer(1);
24 my @genes = $factory->run($hmmfile, $genomic_seq);
25
27 Genewise is a gene prediction program developed by Ewan Birney
28 http://www.sanger.ac.uk/software/wise2.
29 Available Params:
31 NB: These should be passed without the '-' or they will be ignored,
32 except switches such as 'hmmer' (which have no corresponding value)
33 which should be set on the factory object using the AUTOLOADed methods
34 of the same name.
35 Model [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
37 Alg [-kbyte,-alg]
38 HMM [-hmmer]
39 Output [-gff,-gener,-alb,-pal,-block,-divide]
40 Standard [-help,-version,-silent,-quiet,-errorlog]
41
43 Mailing Lists
44 User feedback is an integral part of the evolution of this and other
45 Bioperl modules. Send your comments and suggestions preferably to one
46 of the Bioperl mailing lists. Your participation is much appreciated.
47 bioperl-l@bioperl.org - General discussion
49 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
50 Support
52 Please direct usage questions or support issues to the mailing list:
53 bioperl-l@bioperl.org
55 rather than to the module maintainer directly. Many experienced and
57 reponsive experts will be able look at the problem and quickly address
58 it. Please include a thorough description of the problem with code and
59 data examples if at all possible.
60 Reporting Bugs
62 Report bugs to the Bioperl bug tracking system to help us keep track
63 the bugs and their resolution. Bug reports can be submitted via
64 the web:
65 http://bugzilla.open-bio.org/
67
69 Email: fugui@worf.fugu-sg.org
70
72 Jason Stajich jason-AT-bioperl_DOT_org Keith James kdj@sanger.ac.uk
73
75 The rest of the documentation details each of the object methods.
76 Internal methods are usually preceded with a _
77 program_name
79 Title : program_name
80 Usage : $factory>program_name()
81 Function: holds the program name
82 Returns: string
83 Args : None
84 program_dir
86 Title : program_dir
87 Usage : $factory->program_dir(@params)
88 Function: returns the program directory, obtained from ENV variable.
89 Returns: string
90 Args :
91 version
93 Title : version
94 Usage : exit if $prog->version() < 1.8
95 Function: Determine the version number of the program
96 Example :
97 Returns : float or undef
98 Args : none
99 predict_genes
101 Title : predict_genes
102 Usage : DEPRECATED. Use $factory->run($seq1,$seq2)
103 Function: Predict genes
104 Returns : A Bio::Seqfeature::Gene:GeneStructure object
105 Args : Name of a file containing a set of 2 fasta sequences in the order of
106 peptide and genomic sequences
107 or else 2 Bio::Seq objects.
108 Throws an exception if argument is not either a string (eg a filename)
110 or 2 Bio::Seq objects. If arguments are strings, throws exception if
111 file corresponding to string name can not be found.
112 run
114 Title : run
115 Usage : 2 sequence objects
116 $genes = $factory->run($seq1, $seq2);
117 Function: run
118 Returns : A Bio::Seqfeature::Gene:GeneStructure object
119 Args : Names of a files each containing a fasta sequence in the order
120 of either (peptide sequence, genomic sequence) or (profile HMM,
121 genomic sequence). Alternatively any of the fasta sequence
122 filenames may be substituted with a Bio::Seq object.
123 Throws an exception if argument is not either a string (eg a filename)
125 or Bio::Seq objects. If arguments are strings, throws exception if file
126 corresponding to string name can not be found. Also throws an exception
127 if a profile HMM is expected (the -hmmer genewise switch has been set).
128 _run
130 Title : _run
131 Usage : Internal function, not to be called directly
132 Function: Makes actual system call to a genewise program
133 Example :
134 Returns : L<Bio::SeqFeature::Gene::GeneStructure>
135 Args : Name of a files containing 2 sequences in the order of peptide and genomic
136 _setparams
138 Title : _setparams
139 Usage : Internal function, not to be called directly
140 Function: creates a string of params to be used in the command string
141 Example :
142 Returns : string of params
143 Args :
144 _query_pep_seq
146 Title : _query_pep_seq
147 Usage : Internal function, not to be called directly
148 Function: get/set for the query sequence
149 Example :
150 Returns :
151 Args :
152 _subject_dna_seq
154 Title : _subject_dna_seq
155 Usage : Internal function, not to be called directly
156 Function: get/set for the subject sequence
157 Example :
158 Returns :
159 Args :
161perl v5.12.0 2010-04-29 Bio::Tools::Run::Genewise(3)