1Bio::Tools::Run::GenewiUssee(r3)Contributed Perl DocumenBtiaot:i:oTnools::Run::Genewise(3)
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NAME

6       Bio::Tools::Run::Genewise - Object for predicting genes in a given
7       sequence given a protein
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SYNOPSIS

10         # Build a Genewise alignment factory
11         my $factory = Bio::Tools::Run::Genewise->new();
12
13         # Pass the factory 2 Bio:SeqI objects (in the order of query peptide
14         # and target_genomic).
15
16         # @genes is an array of Bio::SeqFeature::Gene::GeneStructure objects
17         my @genes = $factory->run($protein_seq, $genomic_seq);
18
19         # Alternatively pass the factory a profile HMM filename and a
20         # Bio:SeqI object (in the order of query HMM and target_genomic).
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22         # Set hmmer switch first to tell genewise to expect an HMM
23         $factory->hmmer(1);
24         my @genes = $factory->run($hmmfile, $genomic_seq);
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DESCRIPTION

27       Genewise is a gene prediction program developed by Ewan Birney
28       http://www.sanger.ac.uk/software/wise2.
29
30       Available Params:
31
32       NB: These should be passed without the '-' or they will be ignored,
33       except switches such as 'hmmer' (which have no corresponding value)
34       which should be set on the factory object using the AUTOLOADed methods
35       of the same name.
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37         Model    [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
38         Alg      [-kbyte,-alg]
39         HMM      [-hmmer]
40         Output   [-gff,-gener,-alb,-pal,-block,-divide]
41         Standard [-help,-version,-silent,-quiet,-errorlog]
42

FEEDBACK

44       Mailing Lists
45
46       User feedback is an integral part of the evolution of this and other
47       Bioperl modules. Send your comments and suggestions preferably to one
48       of the Bioperl mailing lists.  Your participation is much appreciated.
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50         bioperl-l@bioperl.org                  - General discussion
51         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
52
53       Reporting Bugs
54
55       Report bugs to the Bioperl bug tracking system to help us keep track
56        the bugs and their resolution.  Bug reports can be submitted via
57        the web:
58
59         http://bugzilla.open-bio.org/
60

AUTHOR - FUGU Student Intern

62       Email: fugui@worf.fugu-sg.org
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CONTRIBUTORS

65       Jason Stajich jason-AT-bioperl_DOT_org Keith James kdj@sanger.ac.uk
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APPENDIX

68       The rest of the documentation details each of the object methods.
69       Internal methods are usually preceded with a _
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71       program_name
72
73        Title   : program_name
74        Usage   : $factory>program_name()
75        Function: holds the program name
76        Returns:  string
77        Args    : None
78
79       program_dir
80
81        Title   : program_dir
82        Usage   : $factory->program_dir(@params)
83        Function: returns the program directory, obtiained from ENV variable.
84        Returns:  string
85        Args    :
86
87       version
88
89        Title   : version
90        Usage   : exit if $prog->version() < 1.8
91        Function: Determine the version number of the program
92        Example :
93        Returns : float or undef
94        Args    : none
95
96       predict_genes
97
98        Title   : predict_genes
99        Usage   : DEPRECATED. Use $factory->run($seq1,$seq2)
100        Function: Predict genes
101        Returns : A Bio::Seqfeature::Gene:GeneStructure object
102        Args    : Name of a file containing a set of 2 fasta sequences in the order of
103                  peptide and genomic sequences
104                  or else 2  Bio::Seq objects.
105
106       Throws an exception if argument is not either a string (eg a filename)
107       or 2 Bio::Seq objects.  If arguments are strings, throws exception if
108       file corresponding to string name can not be found.
109
110       run
111
112        Title   : run
113        Usage   : 2 sequence objects
114                  $genes = $factory->run($seq1, $seq2);
115        Function: run
116        Returns : A Bio::Seqfeature::Gene:GeneStructure object
117        Args    : Names of a files each containing a fasta sequence in the order
118                  of either (peptide sequence, genomic sequence) or (profile HMM,
119                  genomic sequence). Alternatively any of the fasta sequence
120                  filenames may be substituted with a Bio::Seq object.
121
122       Throws an exception if argument is not either a string (eg a filename)
123       or Bio::Seq objects. If arguments are strings, throws exception if file
124       corresponding to string name can not be found. Also throws an exception
125       if a profile HMM is expected (the -hmmer genewise switch has been set).
126
127       _run
128
129        Title   : _run
130        Usage   : Internal function, not to be called directly
131        Function: Makes actual system call to a genewise program
132        Example :
133        Returns : L<Bio::SeqFeature::Gene::GeneStructure>
134        Args    : Name of a files containing 2 sequences in the order of peptide and genomic
135
136       _setparams
137
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
145       _query_pep_seq
146
147        Title   :  _query_pep_seq
148        Usage   :  Internal function, not to be called directly
149        Function:  get/set for the query sequence
150        Example :
151        Returns :
152        Args    :
153
154       _subject_dna_seq
155
156        Title   :  _subject_dna_seq
157        Usage   :  Internal function, not to be called directly
158        Function:  get/set for the subject sequence
159        Example :
160        Returns :
161
162        Args    :
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166perl v5.8.8                       2007-04-19      Bio::Tools::Run::Genewise(3)