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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Parsers/biotiffin.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,259 @@
+=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]>.
+
+=cut
+
+package Bio::EnsEMBL::Funcgen::Parsers::biotiffin;
+
+use strict;
+
+use File::Basename;
+
+# To get files for bioTIFFIN, download the following GFF file (e.g. via wget):
+#
+#  http://td-blade.gurdon.cam.ac.uk/tad26/fly-tiffinScan-tiffin12.dm3.gff.gz
+
+# Thomas Down <[e-mail]>
+
+# 
+# 3R      MotifScanner    TIFDMEM0000001  936391  936401  0.0     +       0
+# 3R      MotifScanner    TIFDMEM0000001  13455911        13455921        0.0     -       0
+# 3R      MotifScanner    TIFDMEM0000001  17062830        17062840        0.0     +       0
+
+use Bio::EnsEMBL::Funcgen::Parsers::BaseExternalParser;
+use Bio::EnsEMBL::DBEntry;
+use Bio::EnsEMBL::Funcgen::ExternalFeature;
+use Bio::EnsEMBL::Utils::Exception qw( throw );
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Parsers::BaseExternalParser);
+
+
+sub new {
+  my $caller = shift;
+  my $class = ref($caller) || $caller;
+
+  my $self = $class->SUPER::new(@_, type => 'BioTiffin');
+
+  #Set default feature_type and feature_set config
+
+  #We need to capture version/release/data of external feature sets.
+  #This can be nested in the description?  Need to add description to feature_set?
+
+  $self->{static_config}{feature_types} = 
+	{
+	 'BioTIFFIN Motif'   => {
+							 name        => 'BioTIFFIN Motif',
+							 class       => 'Regulatory Motif',
+							 description => 'BioTIFFIN motif',
+							}
+	};
+  
+  $self->{static_config}{analyses} = 
+	{
+	 'BioTIFFIN Motif' => { 
+						   -logic_name    => 'BioTIFFIN Motif',
+						   -description   => 'BioTIFFIN regulatory motif database',
+						   -display_label => 'BioTIFFIN motifs',
+						   -displayable   => 1,
+						  },
+	};
+  
+  $self->{static_config}{feature_sets} = 
+	{
+	 'BioTIFFIN Motif' => 
+	 {
+	  feature_set => {
+					  -feature_type => 'BioTIFFIN Motif',
+					  -analysis     => 'BioTIFFIN Motif',
+					 },
+	  xrefs => 0,
+	 }
+	};
+ 
+
+  #Move xref flag here?
+  $self->{config} =  {
+					  'BioTIFFIN Motif' => {
+										file  => $ENV{'EFG_DATA'}.'/input/BioTIFFIN/fly-tiffinScan-tiffin12.dm3.gff',
+										gff_attrs => {
+													  'ID' => 1,
+													 },
+									   },					  
+					 };
+  
+  $self->validate_and_store_config([keys %{$self->{static_config}{feature_sets}}]);
+  $self->set_feature_sets;
+
+  return $self;
+}
+
+
+
+# Parse file and return hashref containing:
+#
+# - arrayref of features
+# - arrayref of factors
+
+
+
+
+sub parse_and_load {
+  my ($self, $files, $old_assembly, $new_assembly) = @_;
+
+  if(scalar(@$files) != 1){
+	throw('You must provide a unique file path to load VISTA features from:\t'.join(' ', @$files));
+  }
+
+
+  my %slice_cache;
+  my $extf_adaptor  = $self->db->get_ExternalFeatureAdaptor;
+  my $dbentry_adaptor = $self->db->get_DBEntryAdaptor;
+  my $ftype_adaptor = $self->db->get_FeatureTypeAdaptor;
+  # this object is only used for projection
+  my $dummy_analysis = new Bio::EnsEMBL::Analysis(-logic_name => 'BioTIFFINProjection');#do we need this?
+  my $species = $self->db->species;
+  if(! $species){
+	throw('Must define a species to define the external_db');
+  }
+  #Just to make sure we hav homo_sapiens and not Homo Sapiens
+  ($species = lc($species)) =~ s/ /_/;
+
+  
+  if(scalar @{$self->import_sets} != 1){
+	throw('biotiffin parser currently only supports one import FeatureSet');
+  }
+
+  my ($import_set) = @{$self->import_sets};
+
+
+  #foreach my $import_set(@{$self->import_sets}){
+  $self->log_header("Parsing $import_set data");
+  
+  my %motif_cache; # name -> factor_id
+  my $config = $self->{'config'}{$import_set};
+  my $fset =  $self->{static_config}{feature_sets}{$import_set}{feature_set};
+  my %gff_attrs =  %{$config->{'gff_attrs'}};
+  
+  
+  # Parse motifs.txt file
+  #my $file =  $config->{'file'};
+  my $file = $files->[0];
+  my $skipped = 0;
+  my $motif_cnt = 0;
+  my $factor_xref_cnt = 0;
+  my $feature_cnt = 0;
+  my $feature_target_cnt = 0;
+	
+  open (FILE, "<$file") || die("Can't open $file\n$!\n");
+
+ LINE: while (my $line = <FILE>) {
+	  chomp $line;
+	  
+	  #GFF3
+		#3R      MotifScanner    TIFDMEM0000001  936391  936401  0.0     +       0
+		#3R      MotifScanner    TIFDMEM0000001  13455911        13455921        0.0     -       0
+    #3R      MotifScanner    TIFDMEM0000001  17062830        17062840        0.0     +       0
+    #3R      MotifScanner    TIFDMEM0000001  17973965        17973975        0.0     +       0
+
+	  #seq_name, source, feature, start, end, score, strand, frame, [attrs]
+	  my ($chromosome, $program, $feature, $start, $end, $score, $strand, undef) = split /\t/o, $line;
+
+	  if(! exists $slice_cache{$chromosome}){
+				
+				if($old_assembly){
+						$slice_cache{$chromosome} = $self->slice_adaptor->fetch_by_region('chromosome', 
+																																							$chromosome, 
+																																							undef, 
+																																							undef, 
+																																							undef, 
+																																							$old_assembly);
+				} else {
+						$slice_cache{$chromosome} = $self->slice_adaptor->fetch_by_region('chromosome', $chromosome);
+				}
+	  }
+		
+	  if(! defined  $slice_cache{$chromosome}){
+				warn "Can't get slice $chromosome for motif $feature;\n";
+				$skipped++;
+				next;
+	  }
+				
+		if(! exists $motif_cache{$feature}){
+				
+				$motif_cache{$feature} = $ftype_adaptor->fetch_by_name($feature);
+				
+				if(! defined $motif_cache{$feature}){
+						
+						($motif_cache{$feature}) = @{$ftype_adaptor->store(Bio::EnsEMBL::Funcgen::FeatureType->new
+																															 (
+																																-name  => $feature,
+																																-class => $fset->feature_type->class,
+																																-description => $fset->feature_type->description,
+																															 ))};						
+						
+						$motif_cnt ++;
+				}
+	  }
+		
+		my $feature_type = $motif_cache{$feature};
+		
+	  #Now build actual feature
+
+	  $feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new
+				(
+				 -display_label => $feature,
+				 -start         => $start,
+				 -end           => $end,
+				 -strand        => (($strand eq '+') ? 1 : -1),
+				 -feature_type  => $feature_type,
+				 -feature_set   => $fset,
+				 -slice         => $slice_cache{$chromosome},
+				);
+		
+		
+	  # project if necessary
+	  if ($new_assembly) {
+				$feature = $self->project_feature($feature, $new_assembly);
+		
+				if(! defined $feature){
+						$skipped ++;
+						next;
+				}
+	  }
+	  
+	  ($feature) = @{$extf_adaptor->store($feature)};
+	  $feature_cnt++;
+
+
+	}
+	
+	close FILE;
+	
+	$self->log("Loaded ".$fset->name);
+	$self->log("$motif_cnt feature types");
+	$self->log("$feature_cnt features");
+	$self->log("Skipped $skipped features");
+
+#}
+
+  return;
+}
+
+1;