MGI_CCDS_Parser.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
package XrefParser::MGI_CCDS_Parser;
 
use strict;
use warnings;
use Carp;
use DBI;
 
use base qw( XrefParser::BaseParser );
 
 
sub run {
 
  my ($self, $ref_arg) = @_;
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $files        = $ref_arg->{files};
  my $verbose      = $ref_arg->{verbose};
  my $dbi          = $ref_arg->{dbi};
  $dbi = $self->dbi unless defined $dbi;
 
  if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
    croak "Need to pass source_id, species_id and file as pairs";
  }
  $verbose |=0;
 
  my $file = @{$files}[0];
 
  my %label;
  my %version;
  my %description;
  my %accession;
 
  my $sql = 'select source_id, priority_description from source where name like "MGI"';
  my $sth = $dbi->prepare($sql);
 
  $sth->execute();
  my ($mgi_source_id, $desc);
  $sth->bind_columns(\$mgi_source_id, \$desc);
  my @arr;
  while($sth->fetch()){
    push @arr, $mgi_source_id;
  }
  $sth->finish;
 
  $sql = "select accession, label, version,  description from xref where source_id in (".join(", ",@arr).")";
 
  $sth = $dbi->prepare($sql);
  $sth->execute();
  my ($acc, $lab, $ver);
  $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
  while (my @row = $sth->fetchrow_array()) {
    if(defined($desc)){
      $accession{$lab} = $acc;
      $label{$acc} = $lab;
      $version{$acc} = $ver;
      $description{$acc} = $desc;
    }
  }
  $sth->finish;
 
 
 
  #
  # Get master xref ids via the ccds label.
  #
 
  $sql = 'select x.label, x.xref_id from xref x, source s where x.source_id = s.source_id and s.name ="CCDS"';
  
  my %ccds_label_to_xref_id;
  $sth = $dbi->prepare($sql);
  $sth->execute();
  my ($xref_id);
  $sth->bind_columns(\$lab, \$xref_id);
  while (my @row = $sth->fetchrow_array()) {
    $ccds_label_to_xref_id{$row[0]} = $row[1];
  }
  $sth->finish;
 
 
 
  my $ua = LWP::UserAgent->new();
  $ua->timeout(10);
  $ua->env_proxy();
  
 
  my $count = 0;
  my $ccds_missing = 0;
  my $entrezgene_missing = 0;
 
  my $mgi_io = $self->get_filehandle($file);
  if ( !defined $mgi_io ) {
    print STDERR "ERROR: Could not open $file\n";
    return 1;    # 1 is an error
  }
 
    #
    #
    ##chromosome    g_accession gene    gene_id ccds_id ccds_status cds_strand  cds_from    cds_to  cds_locations   match_type
    #1  NC_000067.5 Xkr4    497097  CCDS14803.1 Public  -   3206102 3661428 [3206102-3207048, 3411782-3411981, 3660632-3661428] Identical
    #1  NC_000067.5 Rp1h    19888   CCDS14804.1 Public  -   4334680 4342905 [4334680-4340171, 4341990-4342161, 4342282-4342905] Identical
    while (my $line = $mgi_io->getline()) {
      my($chrom, $g_acc, $gene_name, $entrez_id, $ccds, @junk) = split(/\t/,$line);
      if(defined($ccds_label_to_xref_id{$ccds})){ 
    if(defined($accession{$gene_name}) and
       defined($label{$accession{$gene_name}})){
      my $acc = $accession{$gene_name};
      $self->add_dependent_xref({ master_xref_id => $ccds_label_to_xref_id{$ccds},
                      acc            => $acc,
                      version        => $version{$acc},
                      label          => $label{$acc},
                      desc           => $description{$acc},
                      source_id      => $source_id,
                                      dbi            => $dbi,
                      species_id     => $species_id });
 
      $count++;
    }
    else{
      $entrezgene_missing++;
    }
      }
      else{
    $ccds_missing++;
      }
    }
  print "$ccds_missing ccds not resolved, $entrezgene_missing mgi not found. Added $count MGI xrefs via CCDS\n" if($verbose);
  return 0;
}
 
1;