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