diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/Parsers/GFF.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Parsers/GFF.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,195 @@
+#
+# EnsEMBL module for Bio::EnsEMBL::Funcgen::Parsers::GFF
+#
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2011 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+#Could this be based on a Generic Flat file parser?
+
+=head1 NAME
+
+Bio::EnsEMBL::Funcgen::Parsers::GFF
+
+=head1 SYNOPSIS
+
+  my $parser_type = "Bio::EnsEMBL::Funcgen::Parsers::GFF";
+  push @INC, $parser_type;
+  my $imp = $class->SUPER::new(@_);
+
+
+=head1 DESCRIPTION
+
+This is a definitions class which should not be instatiated directly, it 
+normally set by the Importer as the parent class.  GFF contains meta 
+data and methods specific to data in bed format, to aid 
+parsing and importing of experimental data.
+
+=cut
+
+package Bio::EnsEMBL::Funcgen::Parsers::GFF;
+
+use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate );
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use strict;
+
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Parsers::ExperimentalSet);
+
+=head2 new
+
+  Example    : my $self = $class->SUPER::new(@_);
+  Description: Constructor method for GFF class
+  Returntype : Bio::EnsEMBL::Funcgen::Parsers::GFF
+  Exceptions : None
+  Caller     : Bio::EnsEMBL::Funcgen::Importer
+  Status     : at risk
+
+=cut
+
+
+sub new{
+  my $caller = shift;
+  
+  my $class = ref($caller) || $caller;
+
+  #define default fields here and pass
+  #We also need to be able to take custom attrs mappings
+
+  #keys are array index of field, key are Feature paramter names
+  #reverse this?
+  #Unless we have a compound field which we name accordingly
+  #And then call e.g. parse_attrs
+  #Which will return a hash with the relevant Feature attributes
+
+  #Is splitting this up simply going to make the parse slower due to acessor methods?
+
+  #Pass or just set directly here?
+  #<seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
+
+
+  #Some of these may be highly redundant due to the nature of the data.
+  #We can hash things to lessen the impact but we're still going to be checking if exists for each one
+  #No way around this?  Unless it is marginally faster to set a permanent type and then only check a boolean.
+  #Yes there is, this is the exhaustive GFF definition, we can just redefine or delete some entries dynamically to
+  #avoid ever considering a particular field index.
+
+
+  #Don't need any of this? Can we simply define process fields?
+  #This will remove the ability to define custom formats
+  #But then again we can only have custom format if it has ensembl compliant data
+  #i.e. no preprocessing has to be done before populating the feature_params hash
+
+  #my %fields = (
+#				0 => 'fetch_slice',
+#				1 => 'get_source',
+#				2 => 'get_feature_type',
+#				3 => '-start',
+	#			4 => '-end',
+#				5 => '-strand',#Will most likely be , need to convert to -.+ > -1 0 1
+				#6 => 'frame',#will most likely be .
+#				7 => 'get_attributes',
+#			   );
+
+  #We want to be able to define mappings between attributes and fields
+  #we're basically just dealing with display_label for annotated_feature
+  #e.g -display_label_format => ID+ACC
+  #Or maybe format of several fields and attrs + text?
+  #We need a separator which will not be used in the GFF attr names
+  #we also need to be able to differentiate
+  #First check standard GFF field, then check attrs
+  ##No no no, just have method, generate display label
+  #forget this for now and just use one field
+
+  my $display_label_field = 'ID';#default
+
+  #We still need to define the field name here as a global hash to allow this display_label_field look up.
+
+
+  my $self  = $class->SUPER::new(@_);#, -fields => \%fields);
+  
+  ($display_label_field) = rearrange(['DISPLAY_LABEL_FIELD'], @_);
+
+  #We need to define meta header method, starting with '##'
+  #Also need to skip comments '#' at begining or end of line
+  #Do we also need to skip field header? No methinks not.
+
+  #Define result method
+ # $self->{'file_ext'} => 'gff';#Could use vendor here?
+  
+  #define this if we want to override the generic method in Simple
+  #$self->{'config'}{'results_data'} => ["and_import_gff"];  
+
+  $self->display_label_field($display_label_field);
+
+
+  return $self;
+}
+
+
+=head2 set_config
+
+  Example    : my $self->set_config;
+  Description: Sets attribute dependent config
+  Returntype : None
+  Exceptions : None
+  Caller     : Bio::EnsEMBL::Funcgen::Importer
+  Status     : at risk
+
+=cut
+
+
+sub set_config{
+  my $self = shift;
+
+  $self->SUPER::set_config;
+
+  #GFF specific stuff here.
+
+  return;
+}
+
+#Need to implement this!
+sub parse_line{
+  my ($self, $line) = @_;
+
+  #return if $line ~=
+
+ #my %fields = (
+#				0 => 'fetch_slice',
+#				1 => 'get_source',
+#				2 => 'get_feature_type',
+#				3 => '-start',
+	#			4 => '-end',
+#				5 => '-strand',#Will most likely be , need to convert to -.+ > -1 0 1
+				#6 => 'frame',#will most likely be .
+#				7 => 'get_attributes',
+#			   );
+
+
+
+  my ($chr, $start, $end, $pid, $score) = split/\t/o, $line;			
+  
+  #we need to return feature_params and seq if defined?
+
+}
+ 
+
+
+1;