comparison variant_effect_predictor/Bio/EnsEMBL/Funcgen/Parsers/cisred.pm @ 0:1f6dce3d34e0

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=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::cisred;

use strict;

use File::Basename;

# To get files for CisRed data, download the following 2 files (e.g. via wget):
#
# http://www.cisred.org/content/databases_methods/human_2/data_files/motifs.txt
#
# http://www.cisred.org/content/databases_methods/human_2/data_files/search_regions.txt


#No longer valid urls, now use the following for ensembl formats for all species:
#http://www.bcgsc.ca/downloads/cisred/temp/cisRED4Ensembl/
#naminf may not be obvious, may have to cross reference with above previous urls to get build info

# Format of motifs.txt (note group_name often blank)

#name    chromosome      start   end     strand  group_name      ensembl_gene
#craHsap1        1       168129978       168129997       -1      1       ENSG00000000457
#craHsap2        1       168129772       168129781       -1      2       ENSG00000000457
#craHsap3        1       168129745       168129756       -1      3       ENSG00000000457
#craHsap4        1       168129746       168129753       -1      4       ENSG00000000457
#craHsap5        1       168129745       168129752       -1      5       ENSG00000000457
#craHsap6        1       168129741       168129757       -1      6       ENSG00000000457


# Format of search_regions.txt
# name	chromosome	start	end	strand	ensembl_gene_id
# 1	17	39822200	39824467	-1	ENSG00000005961
# 8	17	23151483	23153621	-1	ENSG00000007171
# 14	1	166434638	166437230	-1	ENSG00000007908
# 19	1	23602820	23605631	-1	ENSG00000007968


use Bio::EnsEMBL::Funcgen::Parsers::BaseExternalParser;
use Bio::EnsEMBL::DBEntry;
use Bio::EnsEMBL::Funcgen::ExternalFeature;
use Bio::EnsEMBL::Utils::Exception qw( throw );


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 => 'cisRED');

  #Set default feature_type and feature_set config
  $self->{static_config}{feature_types} = 
	{
	 'cisRED Search Region'   => {
								  -name        => 'cisRED Search Region',
								  -class       => 'Search Region',
								  -description => 'cisRED search region',
								 },
	 'cisRED Motif' => {
						-name        => 'cisRED Motif',
						-class       => 'Regulatory Motif',
						-description => 'cisRED atomic motif',
					   },
	};
  
  $self->{static_config}{analyses} =
	{
	 cisRED => { 
				-logic_name    => 'cisRED',
				-description   => 'cisRED motif search (www.cisred.org)',
				-display_label => 'cisRED',
				-displayable   => 1,
			   },
	};
  
  $self->{static_config}{feature_sets} = 
	{
	 'cisRED search regions' => 
	 {
	  analyses      => $self->{static_config}{analyses},
	  feature_types => $self->{static_config}{feature_types},
	  feature_set   => {
                        #feature_type and analysis here are the keys from above
                        -feature_type  => 'cisRED Search Region',
						-display_label => 'cisRED searches',
						-analysis      => 'cisRED',
					   },
	  xrefs => 1,
	 },
	 
	 
	 'cisRED motifs' => 
	 {
	  analyses      => $self->{static_config}{analyses},
	  feature_types => $self->{static_config}{feature_types},
	  feature_set => {
                      #feature_type and analysis here are the keys from above
					  -feature_type      => 'cisRED Motif',
					  -analysis          => 'cisRED',
					 },
	  xrefs => 1,
	 },
	};
 
  #$self->validate_and_store_feature_types;
  $self->validate_and_store_config([keys %{$self->{static_config}{feature_sets}}]);
  $self->set_feature_sets;

  return $self;
}





# Parse file and return hashref containing:
#
# - arrayref of features
# - arrayref of factors


#To do
# 1 This needs to take both file names, motifs, then search regions. Like the Bed/GFF importers do.


sub parse_and_load {
  my ($self, $files, $old_assembly, $new_assembly) = @_;
  $self->log_header("Parsing cisRED data");

   if(scalar(@$files) != 2){
	 throw('You must currently define a motif and search file to load cisRED features from:\t'.join(' ', @$files));
  }


  my $analysis_adaptor = $self->db->get_AnalysisAdaptor();
  #my %features_by_group; # name -> factor_id
  my %groups;
  my %slice_cache;
  my $extf_adaptor  = $self->db->get_ExternalFeatureAdaptor;
  my $dbentry_adaptor = $self->db->get_DBEntryAdaptor;
  my $ftype_adaptor = $self->db->get_FeatureTypeAdaptor;
  #my $display_name_cache = $self->build_display_name_cache('gene');
  # this object is only used for projection
  my $dummy_analysis = new Bio::EnsEMBL::Analysis(-logic_name => 'CisREDProjection');

  # ----------------------------------------
  # We need a "blank" factor for those features which aren't assigned factors
  # Done this way to maintain referential integrity
  #my $blank_factor_id = $self->get_blank_factor_id($db_adaptor);

 #More validation of files here?
  my ($motif_file)  = grep(/motif/,  @$files);
  my ($search_file) = grep(/search/, @$files);
  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/ /_/;


  # Parse motifs.txt file
  $self->log_header("Parsing cisRED motifs from $motif_file");
  my $skipped = 0;
  my $skipped_xref = 0;
  #my $coords_changed = 0;
  my $cnt = 0;
  my $set = $self->{static_config}{feature_sets}{'cisRED motifs'}{feature_set};


   
  open (FILE, "<$motif_file") || die "Can't open $motif_file";
  <FILE>; # skip header

  while (<FILE>) {
    next if ($_ =~ /^\s*\#/o || $_ =~ /^\s*$/o);
	chomp;

	#name    chromosome      start   end     strand  group_name      ensembl_gene
	#craHsap1        1       168129978       168129997       -       crtHsap40066,crtHsap40060       ENSG00000000457
	#craHsap2        1       168129772       168129781       -       crtHsap40068,crtHsap40193,crtHsap40130  ENSG00000000457

	#So we only ever have one atomic motif, which may belong to several groups
	#Do not store atmoic motifs as feature types as this is the actual feature
	#simply use the feature_set->feature_type and store the atmoic motif id as the name


    my ($motif_name, $chromosome, $start, $end, $strand, $groups, $gene_id) = split/\t/o;
    #($gene_id) = $gene_id =~ /(ENS.*G\d{11})/;
	my @group_names = split/,/, $groups;

	#These are stranded features, so either - or +, never 0;
	$strand = ($strand eq '-') ? -1 : 1;

	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 $motif_name\n";
	  $skipped++;
	  next;
	}
	

	#get feature_type first

	#we are not maintaining this link in the DB!
	#Do we need another xref for this or a different table?

	
	#if ($group_name && $group_name ne '' && $group_name !~ /\s/o) {
#
#	  if(! exists $features_by_group{$group_name}){
#		$features_by_group{$group_name} = $ftype_adaptor->fetch_by_name('crtHsap'.$group_name);
#
#		if(! defined $features_by_group{$group_name}){
#		  ($features_by_group{$group_name}) = @{$ftype_adaptor->store(Bio::EnsEMBL::Funcgen::FeatureType->new
#																	  (
#																	   -name  => 'crtHsap'.$group_name,
#																	   -class => 'Regulatory Motif',
#																	   -description => 'cisRED group',
#																	  ))};
#		}
#	  }
#	}
	#}else{
	#  throw("Found cisRED feature $motif_name with no group_name, unable to defined feature_type");
	#}

	foreach my $group(@group_names){

	  next if exists $groups{$group};

	  #else store the new group as a feature_type and set $group to be the feature_type
	  ($group) = @{$ftype_adaptor->store(Bio::EnsEMBL::Funcgen::FeatureType->new
										 (
										  -name  => $group,
										  -class => 'Regulatory Motif',
										  -description => 'cisRED group',
										 ))};
	}



	#my $ftype = (defined $features_by_group{$group_name}) ? $features_by_group{$group_name} : $self->{'feature_sets'}{'cisRED group motifs'}->feature_type;


    my $feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new
      (
	   -display_label => $motif_name,
	   -start         => $start,
	   -end           => $end,
	   -strand        => $strand,
       #-feature_type  => $ftype,
	   -associated_feature_types => \@group_names,
	   -feature_set   => $set,
	   -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)};
	$cnt++;



	#We don't care so much about loading features for retired Genes here
	#as the Genes are only used to define the search regions
	#Not a direct alignment as with the miRanda set

	#However, adding an xref will create dead link in the browser
	
	#Build Xref here
	if (! $gene_id) {
      warn("No xref available for motif $motif_name\n");
      $skipped_xref++;
      next;
    }

	my $display_name = $self->get_core_display_name_by_stable_id($self->db->dnadb, $gene_id, 'gene');

	#Handle release/version in xref version as stable_id version?

	my $dbentry = Bio::EnsEMBL::DBEntry->new
    (
     -dbname                 => $species.'_core_Gene',
     #-release                => $self->db->_get_schema_build($self->db->dnadb),
     #-release                => '49_36b',#harcoded for human
     -release                => '49_37b', #hardcoded for mouse
     -status                 => 'KNOWNXREF',
     #-display_label_linkable => 1,
     -db_display_name        => 'EnsemblGene',
     -type                   => 'MISC',#this is external_db.type
     -primary_id             => $gene_id,
     -display_id             => $display_name,
     -info_type              => 'MISC',
     -info_text              => 'GENE',
     -linkage_annotation     => 'cisRED motif gene',
     -analysis               => $set->analysis,
     #could have version here if we use the correct dnadb to build the cache
    );
	$dbentry_adaptor->store($dbentry, $feature->dbID, 'ExternalFeature', 1);#1 is ignore release flag
  }
  
	
  close FILE;

 $self->log("Stored $cnt cisRED ExternalFeature motif");
 $self->log("Skipped $skipped cisRED ExternalFeature motif imports");
 $self->log("Skipped an additional $skipped_xref DBEntry imports");

  #Now store states
  foreach my $status(qw(DISPLAYABLE MART_DISPLAYABLE)){
	$set->adaptor->store_status($status, $set);
  }
  


  # ----------------------------------------
  # Search regions 
  # read search_regions.txt from same location as $file

  #my $search_regions_file = dirname($file) . "/search_regions.txt";
  #my $search_file;
  #($search_regions_file = $file) =~ s/motifs/searchregions/;

  $skipped = 0;
  $cnt = 0;
  $skipped_xref = 0;
  $set = $self->{static_config}{feature_sets}{'cisRED search regions'}{feature_set};

  $self->log_header("Parsing cisRED search regions from $search_file");
  open (SEARCH_REGIONS, "<$search_file") || die "Can't open $search_file";
  <SEARCH_REGIONS>; # skip header

  while (<SEARCH_REGIONS>) {
    chomp;
    my ($id, $chromosome, $start, $end, $strand, $gene_id) = split;
    my $display_id = $self->get_core_display_name_by_stable_id($self->db->dnadb, $gene_id, 'gene');
	my $name = "CisRed_Search_$id";

	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 search region $name\n";
	  next;
	}
	


	

    my $search_feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new
      (
       -display_label => $name,
       -start         => $start,
       -end           => $end,
       -strand        => $strand,
       -feature_set   => $set,
       -slice         => $slice_cache{$chromosome},
      );
																


    # project if necessary
    if ($new_assembly) {
      $search_feature = $self->project_feature($search_feature);
	  
	  if(! defined $search_feature){
		$skipped ++;
		next;
	  }
	}

	$extf_adaptor->store($search_feature);
	$cnt++;

	#Build Xref here
	#need to validate gene_id here!!

	if (! $gene_id) {
      warn("Can't get internal ID for $gene_id\n");
      $skipped_xref++;
      next;
    }

	my $display_name = $self->get_core_display_name_by_stable_id($self->db->dnadb, $gene_id, 'gene');
	
	my $dbentry = Bio::EnsEMBL::DBEntry->new
    (
     -dbname                 => $species.'_core_Gene',
     #-release                => $self->db->dnadb->dbc->dbname,
     -status                 => 'KNOWNXREF',
     #-display_label_linkable => 1,
     #-db_display_name        => $self->db->dnadb->dbc->dbname,
     -db_display_name        => 'EnsemblGene',
     -type                   => 'MISC',
     -primary_id             => $gene_id,
     -display_id             => $display_name,
     -info_type              => 'MISC',
     -info_text              => 'GENE',
     -linkage_annotation     => 'cisRED search region gene',#omit?
     -analysis               => $set->analysis,
     #could have version here if we use the correct dnadb to build the cache
    );
	$dbentry_adaptor->store($dbentry, $search_feature->dbID, 'ExternalFeature', 1);#1 is ignore release flag  
  }

  close(SEARCH_REGIONS);

  
  $self->log("Stored $cnt cisRED search region ExternalFeatures");
  $self->log("Skipped $skipped cisRED search region ExternalFeatures");
  $self->log("Skipped an additional $skipped_xref cisRED search region DBEntry imports");

  #No MART_DISPLAYABLE here
  $set->adaptor->store_status('DISPLAYABLE', $set);

  
  #print "$coords_changed features had their co-ordinates changed as a result of assembly mapping.\n" if ($new_assembly);

  return;

}



1;