Public Member Functions
public Int	run ()

public Boolean	is_file_header_valid ()

Detailed Description

Description

This parser will read and create dependent xrefs from a simple
comma-delimited file downloaded from the EntrezGene database.

Synopsis

my $parser = XrefParser::EntrezGeneParser->new($db->dbh);
$parser->run({
  source_id  => 11,
  species_id => 9606,
  files      => [ "gene_info.gz" ],
});

Definition at line 21 of file EntrezGeneParser.pm.

Member Function Documentation

◆ is_file_header_valid()

public Boolean XrefParser::EntrezGeneParser::is_file_header_valid ( )

  Arg [1..N] : list of column names provided by Text::CSV::getline()
  Example    :

if ( ! is_file_header_valid( $csv->getline( $fh ) ) {
                confess 'Bad header';
              }

  Description: Verifies if the header of a EntrezGene file follows expected
               syntax.
  Return type: boolean
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

click to view

◆ run()

public Int XrefParser::EntrezGeneParser::run ( )

  Arg [1]    : HashRef standard list of arguments from ParseSource
  Description: Add dependent xrefs from EntrezGene to the xref database
  Return type: Int; 0 upon success
  Exceptions : throws on all processing errors
  Caller     : ParseSource in the xref pipeline

Code:

click to view

sub run {
 
  my ( $self, $ref_arg ) = @_;
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $species_name = $ref_arg->{species};
  my $files        = $ref_arg->{files};
  my $verbose      = $ref_arg->{verbose} // 0;
  my $dbi          = $ref_arg->{dbi} // $self->dbi;
 
  if ( ( !defined $source_id ) or
       ( !defined $species_id ) or
       ( !defined $files ) )
    {
    confess 'Need to pass source_id, species_id and files';
  }
 
  my $file = @{$files}[0];
 
  my $wiki_source_id =
    $self->get_source_id_for_source_name( 'WikiGene', undef, $dbi );
 
  my $eg_io = $self->get_filehandle($file);
  if ( !defined $eg_io ) {
    confess "Could not open $file";
  }
 
  my $input_file = Text::CSV->new({
    sep_char => "\t",
    empty_is_undef => 1,
    allow_loose_quotes => 1
  })
    || confess "Cannot use file $file: " . Text::CSV->error_diag();
 
  # process header
  if ( ! is_file_header_valid( $input_file->header( $eg_io ) ) ) {
    confess "Malformed or unexpected header in EntrezGene file '${file}'";
  }
 
  my $xref_count = 0;
  my $syn_count  = 0;
  my %seen;    # record already processed xrefs
 
  # read data and load xrefs
 RECORD:
  while ( my $data = $input_file->getline($eg_io) ) {
    my ( $tax_id, $acc, $symbol, undef, $synonyms, undef, undef, undef, $desc ) = @{ $data };
 
    # species_id corresponds to the species taxonomy id, see:
    # https://github.com/Ensembl/ensembl-xref/pull/31#issuecomment-445838474
    if ( $tax_id ne $species_id ) {
      next RECORD;
    }
 
    if ( exists $seen{$acc} ) {
      next RECORD;
    }
 
    $self->add_xref({
      acc        => $acc,
      label      => $symbol,
      desc       => $desc,
      source_id  => $source_id,
      species_id => $species_id,
      dbi        => $dbi,
      info_type  => 'DEPENDENT'
    });
    $self->add_xref({
      acc        => $acc,
      label      => $symbol,
      desc       => $desc,
      source_id  => $wiki_source_id,
      species_id => $species_id,
      dbi        => $dbi,
      info_type  => 'DEPENDENT'
    });
    $xref_count += 1;
 
    my @syn = split qr{ \| }msx, $synonyms;
    foreach my $synonym ( @syn ) {
      if ( $synonym ne q{-} ) {
        $self->add_to_syn( $acc, $source_id, $synonym, $species_id, $dbi );
        $syn_count += 1;
      }
    }
 
    $seen{$acc} = 1;
  } ## end while ( my $data = $input_file...)
 
  $input_file->eof ||
    confess "Error parsing file $file, should be EOF: " . $input_file->error_diag();
  $eg_io->close();
 
  if ( $verbose ) {
    print $xref_count . " EntrezGene Xrefs added with $syn_count synonyms\n";
  }
 
  return 0;
} ## end sub run

The documentation for this class was generated from the following file:

ensembl/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm

Public Member Functions

Detailed Description

Description

Synopsis

Member Function Documentation

◆ is_file_header_valid()

◆ run()