comparison variant_effect_predictor/Bio/Factory/SeqAnalysisParserFactory.pm @ 0:1f6dce3d34e0

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date Thu, 11 Apr 2013 02:01:53 -0400
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1 # $Id: SeqAnalysisParserFactory.pm,v 1.9 2002/12/01 00:05:20 jason Exp $
2 #
3 # BioPerl module for Bio::Factory::SeqAnalysisParserFactory
4 #
5 # Cared for by Jason Stajich <jason@bioperl.org>,
6 # and Hilmar Lapp <hlapp@gmx.net>
7 #
8 # Copyright Jason Stajich, Hilmar Lapp
9 #
10 # You may distribute this module under the same terms as perl itself
11
12 # POD documentation - main docs before the code
13
14 =head1 NAME
15
16 Bio::Factory::SeqAnalysisParserFactory - class capable of
17 creating SeqAnalysisParserI compliant parsers
18
19 =head1 SYNOPSIS
20
21 # initialize an object implementing this interface, e.g.
22 $factory = Bio::Factory::SeqAnalysisParserFactory->new();
23 # find out the methods it knows about
24 print "registered methods: ",
25 join(', ', keys($factory->driver_table())), "\n";
26 # obtain a parser object
27 $parser = $factory->get_parser(-input=>$inputobj,
28 -params=>[@params],
29 -method => $method);
30 # $parser is an object implementing Bio::SeqAnalysisParserI
31 # annotate sequence with features produced by parser
32 while(my $feat = $parser->next_feature()) {
33 $seq->add_SeqFeature($feat);
34 }
35
36 =head1 DESCRIPTION
37
38 This is a factory class capable of instantiating SeqAnalysisParserI
39 implementing parsers.
40
41 The concept behind this class and the interface it implements
42 (Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result parsing
43 in high-throughput automated sequence annotation pipelines. See
44 Bio::SeqAnalysisParserI for more documentation of this concept.
45
46 You can always find out the methods an instance of this class knows
47 about by the way given in the SYNOPSIS section. By default, and
48 assuming that the documentation is up-to-date, this will comprise of
49 genscan, mzef, estscan, blast, hmmer, gff, and sim4 (all case-insensitive).
50
51 =head1 FEEDBACK
52
53 =head2 Mailing Lists
54
55 User feedback is an integral part of the evolution of this
56 and other Bioperl modules. Send your comments and suggestions preferably
57 to one of the Bioperl mailing lists.
58 Your participation is much appreciated.
59
60 bioperl-l@bioperl.org - General discussion
61 http://bio.perl.org/MailList.html - About the mailing lists
62
63 =head2 Reporting Bugs
64
65 Report bugs to the Bioperl bug tracking system to help us keep track
66 the bugs and their resolution.
67 Bug reports can be submitted via email or the web:
68
69 bioperl-bugs@bio.perl.org
70 http://bugzilla.bioperl.org/
71
72 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
73
74 Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
75
76 =head1 APPENDIX
77
78 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
79
80 =cut
81
82 package Bio::Factory::SeqAnalysisParserFactory;
83 use strict;
84
85 use Bio::Factory::SeqAnalysisParserFactoryI;
86 use Bio::Factory::DriverFactory;
87
88 use vars qw(@ISA);
89 @ISA = qw(Bio::Factory::DriverFactory Bio::Factory::SeqAnalysisParserFactoryI);
90
91 BEGIN {
92 Bio::Factory::DriverFactory->register_driver
93 (
94 "genscan" => "Bio::Tools::Genscan",
95 "mzef" => "Bio::Tools::MZEF",
96 "estscan" => "Bio::Tools::ESTScan",
97 "bplite" => "Bio::Tools::BPlite",
98 "blast" => "Bio::Tools::BPlite",
99 "hmmer" => "Bio::Tools::HMMER::Result",
100 "gff" => "Bio::Tools::GFF",
101 "sim4" => "Bio::Tools::Sim4::Results",
102 "epcr" => "Bio::Tools::EPCR",
103 "exonerate" => "Bio::Tools::Exonerate",
104 );
105 }
106
107 sub new {
108 my ($class, @args) = @_;
109 my $self = $class->SUPER::new(@args);
110
111 # no per-object initialization right now - registration of default drivers
112 # is only done once when the module is loaded
113 return $self;
114 }
115
116 =head2 get_parser
117
118 Title : get_parser
119 Usage : $factory->get_parser(-input=>$inputobj,
120 [ -params=>[@params] ],
121 -method => $method)
122 Function: Creates and returns a parser object for the given input and method.
123 Both file names and streams (filehandles) are allowed.
124
125 Parameters (-params argument) are passed on to the parser object
126 and therefore are specific to the parser to be created.
127 Example :
128 Returns : A Bio::SeqAnalysisParserI implementing object. Exception if
129 creation of the parser object fails.
130 Args : B<input> - object/file where analysis results are coming from,
131 B<params> - parameter to use when parsing/running analysis
132 B<method> - method of analysis
133
134 =cut
135
136 sub get_parser {
137 my ($self, @args) = @_;
138 my $parser;
139 my $module;
140
141 my ($input, $params, $method) =
142 $self->_rearrange([qw(INPUT PARAMS METHOD)], @args);
143
144 # retrieve module name for requested method
145 $method = lc $method; # method is case-insensitive
146 $module = $self->get_driver($method);
147 if(! defined($module)) {
148 $self->throw("Analysis parser driver for method $method not registered.");
149 }
150 # load module
151 $self->_load_module($module); # throws an exception on failure to load
152 # make sure parameters is not undef
153 $params = [] if( !defined $params );
154 # figure out input method (file or stream)
155 my $inputmethod = '-file';
156 if( ref($input) =~ /GLOB/i ) {
157 $inputmethod = '-fh';
158 }
159 # instantiate parser and return the result
160 $parser = $module->new($inputmethod => $input, @$params);
161 if(! $parser->isa('Bio::SeqAnalysisParserI')) {
162 $self->throw("Driver $module registered for method $method does not implement Bio::SeqAnalyisParserI. How come?");
163 }
164 return $parser;
165 }
166
167 1;