Raw content of Bio::EnsEMBL::Funcgen::Parsers::cisred
<![CDATA[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#No longer valid urls, now use the following for ensembl formats for all species: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(@_);
#Set default feature_type and feature_set config
$self->{'feature_types'} = {
'cisRED Search Region' => {
name => 'cisRED Search Region',
class => 'Region',
description => 'cisRED search region',
},
'cisRED Motif' => {
name => 'cisRED Motif',
class => 'Regulatory Motif',
description => 'cisRED atomic motif',
},
};
$self->{feature_sets} = {
'cisRED search regions' => {
feature_type => \$self->{'feature_types'}{'cisRED Search Region'},
display_label => 'cisRED searches',
analysis =>
{
-logic_name => 'cisRED',
-description => 'cisRED motif search (www.cisred.org)',
-display_label => 'cisRED',
-displayable => 1,
},
xrefs => 1,
},
'cisRED motifs' => {
feature_type => \$self->{'feature_types'}{'cisRED Motif'},
#display_label => 'cisRED motifs',#defaults to name
analysis =>
{
-logic_name => 'cisRED',
-description => 'cisRED motif search (www.cisred.org)',
-display_label => 'cisRED',
-displayable => 1,
},
xrefs => 1,
},
};
$self->validate_and_store_feature_types;
$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");
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 $cnt = 0;
open (FILE, "<$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 => $self->{'feature_sets'}{'cisRED motifs'},
-slice => $slice_cache{$chromosome},
);
# project if necessary
if ($new_assembly) {
$feature = $self->project_feature($feature, $new_assembly);
if(! defined $feature){
$skipped ++;
next;
}
#$coords_changed++ if ($projected_feature->start() != $start || $projected_feature->end() != $end);
}
($feature) = @{$extf_adaptor->store($feature)};
$cnt++;
#need to validate gene_id here
#retrieve from db?
#could have version here if we use the correct dnadb to build the cache
#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->dnadb->dbc->dbname,
-status => 'KNOWNXREF',
#-display_label_linkable => 1,
-#db_display_name => $self->db->dnadb->dbc->dbname,
-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',
#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");
# ----------------------------------------
# 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;
$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_type => $self->{'feature_sets'}{'cisRED search regions'}->feature_type,
-feature_set => $self->{'feature_sets'}{'cisRED search regions'},
-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?
#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 $skipped_xref cisRED search region DBEntry imports");
#print "$coords_changed features had their co-ordinates changed as a result of assembly mapping.\n" if ($new_assembly);
return;
}
1;
]]>