Raw content of Bio::EnsEMBL::Funcgen::Parsers::miranda
<![CDATA[package Bio::EnsEMBL::Funcgen::Parsers::miranda;
use strict;
#This was in the description
#For MSKCC miRanda targets
#Contact is Doron Betel (or maybe Mark Levenstien levenstm@mskcc.org)
#http://www.microrna.org/microrna/getDownloads.do
#Current Human/Mouse/Rat
#This is what we have actually hosted
#For Sanger miRanda targets
#contact svd@sanger.ac.uk stijn van dongen
#From our download page
#http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl
#and then
#ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.gff.homo_sapiens.zip
# #<GROUP> <SEQ> <METHOD> <FEATURE> <CHR> <START> <END> <STRAND> <PHASE> <SCORE>
# Similarity hsa-miR-23b miRanda miRNA_target 1 919788 919807 + . 69 transcript id "ENST00000310998"
# Similarity hsa-miR-23a miRanda miRNA_target 1 919787 919807 + . 71 transcript id "ENST00000310998"
##GROUP SEQ METHOD FEATURE CHR START END STRAND PHASE SCORE PVALUE_OG TRANSCRIPT_ID EXTERNAL_NAME
#Similarity mmu-miR-707 miRanda miRNA_target 2 120824620 120824640 + . 15.3548 2.796540e-02 ENST00000295228 INHBB
#But we now want to host a reduced set from Anton
use Bio::EnsEMBL::Funcgen::Parsers::BaseExternalParser;
use Bio::EnsEMBL::DBEntry;
use Bio::EnsEMBL::Funcgen::ExternalFeature;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::Parsers::BaseExternalParser);
# Parse file and return hashref containing:
#
# - arrayref of features
# - arrayref of factors
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'} = {
'miRanda' => {
name => 'miRanda Target',
class => 'RNA',
description => 'miRanda microRNA target',
},
};
$self->{feature_sets} = {
'miRanda miRNA targets' =>
{
feature_type => \$self->{'feature_types'}{'miRanda'},
display_name => 'miRanda Targets',
analysis =>
{
-logic_name => 'miRanda',
#-description => 'miRanda microRNA target prediction (http://www.microrna.org)',
-description => 'miRanda microRNA target prediction (http://microrna.sanger.ac.uk/targets)',
-display_label => 'miRanda Target',
-displayable => 1,
},
xrefs => 1,
},
};
$self->validate_and_store_feature_types;
$self->set_feature_sets;
return $self;
}
sub parse_and_load{
my ($self, $file, $old_assembly, $new_assembly) = @_;
$self->log_header("Parsing miRanda data from:\t$file");
my $analysis_adaptor = $self->db->get_AnalysisAdaptor();
my $ftype_adaptor = $self->db->get_FeatureTypeAdaptor();
my $extf_adaptor = $self->db->get_ExternalFeatureAdaptor;
my $dbentry_adaptor = $self->db->get_DBEntryAdaptor;
my %features_by_name; # name -> feature_type
my %slice_cache;
# this object is only used for projection
my $dummy_analysis = new Bio::EnsEMBL::Analysis(-logic_name => 'miRandaProjection');
my $skipped = 0;
my $cnt = 0;
my $skipped_xref = 0;
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($species)) =~ s/ /_/;
open (FILE, "<$file") || die "Can't open $file";
while (<FILE>) {
next if ($_ =~ /^\s*\#/o || $_ =~ /^\s*$/o);
#Sanger
##GROUP SEQ METHOD FEATURE CHR START END STRAND PHASE SCORE PVALUE_OG TRANSCRIPT_ID EXTERNAL_NAME
#Similarity mmu-miR-707 miRanda miRNA_target 2 120824620 120824640 + . 15.3548 2.796540e-02 ENST00000295228 INHBB
#MSKCC
#UCSC ID mRNA Gene ID miRNA acc miRNA miRNA align alignment gene align align score conservation miRNA start miRNA end gene start gene end %ID %Similar energy organism prediction_date
#uc001abs.1 AK091100 LOC643837 MIMAT0000062 hsa-let-7a uuGAUAUGUUGGAUGAUGGAGu ||: || |:| ||:|||| guCUGCUCACCUUCCUGCCUCa 144 0.615759 2 21 396 417 63 78 0 9606 2008-05-16
#uc001afh.1 NM_001039577 CCNL2 MIMAT0000062 hsa-let-7a uugauAUGUUGGAUGAUGGAGu |::||||| ||:|||| cucacUGUAACCU-CUGCCUCc 147 0.767611 2 18 2290 2310 75 93 0 9606 2008-05-16
my ($group, $seq, $method, $feature, $chr, $start, $end, $strand, undef, undef, undef, $ens_id, $display_name) = split;
$strand = ($strand =~ /\+/o) ? 1 : -1;
##my $id = $ens_id =~ s/[\"\']//g; # strip quotes
my $id = $ens_id.':'.$seq;
if(! exists $slice_cache{$chr}){
if($old_assembly){
$slice_cache{$chr} = $self->slice_adaptor->fetch_by_region('chromosome',
$chr,
undef,
undef,
undef,
$old_assembly);
}else{
$slice_cache{$chr} = $self->slice_adaptor->fetch_by_region('chromosome', $chr);
}
if(! defined $slice_cache{$chr}){
warn "Can't get slice $chr for sequence $id\n";
$skipped++;
next;
}
}
#We can add coding xref to feature type based on the miRbase name
#.e.g hsa-mir-24-1
#However, this isn't stored as an xref
#It is stored in the gene.description
#e.g. hsa-mir-24-1 [Source:miRBase;Acc:MI0000080]
#Not easy to fetch as descriptions not indexed!
#
#Cache/store FeatureType
if(! exists $features_by_name{$seq}){
$features_by_name{$seq} = $ftype_adaptor->fetch_by_name($seq);
if(! defined $features_by_name{$seq}){
($features_by_name{$seq}) = @{$ftype_adaptor->store(Bio::EnsEMBL::Funcgen::FeatureType->new
(
-name => $seq,
-class => 'RNA',
-description => $method.' '.$feature,
))};
}
}
$feature = Bio::EnsEMBL::Funcgen::ExternalFeature->new
(
-display_label => $id,
-start => $start,
-end => $end,
-strand => $strand,
-feature_type => $features_by_name{$seq},
-feature_set => $self->{'feature_sets'}{'miRanda miRNA'},
-slice => $slice_cache{$chr},
);
# project if necessary
if ($new_assembly) {
$feature = $self->project_feature($feature, $new_assembly);
if(! defined $feature){
$skipped ++;
next;
}
}
($feature) = @{$extf_adaptor->store($feature)};
$cnt++;
#Build xref
#This should enever happen, as the search regions are defined by ens transcript
if (! $ens_id) {
warn("No xref available for miRNA $id\n");
$skipped_xref++;
next;
}
#use external_name first, else try and get it from the core DB
#should we just get it from the core DB anyway?
if(! defined $display_name){
$display_name = $self->get_core_display_name_by_stable_id($self->db->dnadb, $ens_id, 'transcript');
}
#Handle release/version in xref version as stable_id version?
my $dbentry = Bio::EnsEMBL::DBEntry->new(
-dbname => $species.'_core_Transcript',
#-release => $self->db->dnadb->dbc->dbname,
-status => 'KNOWNXREF',
#-display_label_linkable => 1,
#-db_display_name => $self->db->dnadb->dbc->dbname,
-db_display_name => 'EnsemblTranscript',
-type => 'MISC',
-primary_id => $ens_id,
-display_id => $display_name,
-info_type => 'MISC',
-info_text => 'TRANSCRIPT',
#-linkage_annotation => 'miRanda miRNA negative influence',
-linkage_annotation => 'miRanda target - negative influence',
#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 miRanda miRNA ExternalFeatures");
$self->log("Skipped $skipped miRanda miRNA imports");
$self->log("Skipped an additional $skipped_xref DBEntry imports");
return;
}
1;
]]>