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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Factory/SeqAnalysisParserFactory.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,167 @@
+# $Id: SeqAnalysisParserFactory.pm,v 1.9 2002/12/01 00:05:20 jason Exp $
+#
+# BioPerl module for Bio::Factory::SeqAnalysisParserFactory
+#
+# Cared for by Jason Stajich <[e-mail]>,
+# and Hilmar Lapp <[e-mail]>
+#
+# Copyright Jason Stajich, Hilmar Lapp
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Factory::SeqAnalysisParserFactory - class capable of
+              creating SeqAnalysisParserI compliant parsers
+
+=head1 SYNOPSIS
+
+    # initialize an object implementing this interface, e.g.
+    $factory = Bio::Factory::SeqAnalysisParserFactory->new();
+    # find out the methods it knows about
+    print "registered methods: ",
+          join(', ', keys($factory->driver_table())), "\n";
+    # obtain a parser object
+    $parser = $factory->get_parser(-input=>$inputobj,
+                                   -params=>[@params],
+		                   -method => $method);
+    # $parser is an object implementing Bio::SeqAnalysisParserI
+    # annotate sequence with features produced by parser
+    while(my $feat = $parser->next_feature()) {
+	$seq->add_SeqFeature($feat);
+    }
+
+=head1 DESCRIPTION
+
+This is a factory class capable of instantiating SeqAnalysisParserI 
+implementing parsers.
+
+The concept behind this class and the interface it implements
+(Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result parsing
+in high-throughput automated sequence annotation pipelines. See
+Bio::SeqAnalysisParserI for more documentation of this concept.
+
+You can always find out the methods an instance of this class knows
+about by the way given in the SYNOPSIS section. By default, and
+assuming that the documentation is up-to-date, this will comprise of
+genscan, mzef, estscan, blast, hmmer, gff, and sim4 (all case-insensitive).
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this
+and other Bioperl modules. Send your comments and suggestions preferably
+ to one of the Bioperl mailing lists.
+Your participation is much appreciated.
+
+  [e-mail]                - General discussion
+  http://bio.perl.org/MailList.html    - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+ the bugs and their resolution.
+ Bug reports can be submitted via email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp, Jason Stajich
+
+Email Hilmar Lapp E<lt>[e-mail]<gt>, Jason Stajich E<lt>[e-mail]<gt>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+package Bio::Factory::SeqAnalysisParserFactory;
+use strict;
+
+use Bio::Factory::SeqAnalysisParserFactoryI;
+use Bio::Factory::DriverFactory;
+
+use vars qw(@ISA);
+@ISA = qw(Bio::Factory::DriverFactory Bio::Factory::SeqAnalysisParserFactoryI);
+
+BEGIN {
+    Bio::Factory::DriverFactory->register_driver
+	(
+	 "genscan"   => "Bio::Tools::Genscan",
+	 "mzef"      => "Bio::Tools::MZEF",
+	 "estscan"   => "Bio::Tools::ESTScan",
+	 "bplite"    => "Bio::Tools::BPlite",
+	 "blast"     => "Bio::Tools::BPlite",
+	 "hmmer"     => "Bio::Tools::HMMER::Result",
+	 "gff"       => "Bio::Tools::GFF",
+	 "sim4"      => "Bio::Tools::Sim4::Results",
+	 "epcr"      => "Bio::Tools::EPCR", 
+	 "exonerate" => "Bio::Tools::Exonerate",
+	 );
+}
+
+sub new {
+    my ($class, @args) = @_;
+    my $self = $class->SUPER::new(@args);
+
+    # no per-object initialization right now - registration of default drivers
+    # is only done once when the module is loaded
+    return $self;
+}
+
+=head2 get_parser
+
+ Title   : get_parser
+ Usage   : $factory->get_parser(-input=>$inputobj, 
+                                [ -params=>[@params] ],
+		                -method => $method)
+ Function: Creates and returns a parser object for the given input and method.
+           Both file names and streams (filehandles) are allowed.
+
+           Parameters (-params argument) are passed on to the parser object
+           and therefore are specific to the parser to be created.
+ Example :
+ Returns : A Bio::SeqAnalysisParserI implementing object. Exception if
+           creation of the parser object fails.
+ Args    : B<input>  - object/file where analysis results are coming from,
+	   B<params> - parameter to use when parsing/running analysis
+	   B<method> - method of analysis
+
+=cut
+
+sub get_parser {
+    my ($self, @args) = @_;
+    my $parser;
+    my $module;
+    
+    my ($input, $params, $method) =
+	$self->_rearrange([qw(INPUT PARAMS METHOD)], @args);
+    
+    # retrieve module name for requested method
+    $method = lc $method; # method is case-insensitive
+    $module = $self->get_driver($method);
+    if(! defined($module)) {
+	$self->throw("Analysis parser driver for method $method not registered.");
+    }
+    # load module
+    $self->_load_module($module); # throws an exception on failure to load
+    # make sure parameters is not undef
+    $params = [] if( !defined $params );
+    # figure out input method (file or stream)
+    my $inputmethod = '-file';
+    if( ref($input) =~ /GLOB/i ) {
+	$inputmethod = '-fh';
+    }
+    # instantiate parser and return the result
+    $parser = $module->new($inputmethod => $input, @$params);
+    if(! $parser->isa('Bio::SeqAnalysisParserI')) {
+	$self->throw("Driver $module registered for method $method does not implement Bio::SeqAnalyisParserI. How come?");
+    }
+    return $parser;
+}
+
+1;