ensembl-hive: XrefParser::DBASSParser Class Reference

ensembl-hive 2.7.0

Public Member Functions
public void	run ()

public Boolean	is_file_header_valid ()

Detailed Description

Definition at line 5 of file DBASSParser.pm.

Member Function Documentation

◆ is_file_header_valid()

public Boolean XrefParser::DBASSParser::is_file_header_valid ( )

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

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

  Description: Verifies if the header of a DBASS file follows expected
               syntax and contains expected column names.
  Return type: boolean
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

click to view

◆ run()

public void XrefParser::DBASSParser::run ( )

  Arg [1]    : HashRef standard list of arguments from ParseSource
  Example    :

$dbass_parser->run({ ... });

  Description: Extract DBASS3/DBASS5 entries from a comma-delimited
               file downloaded from the DBASS Web site, then insert
               corresponding xrefs and gene_direct_xref links into the
               xref database.

               The columns of the file should be the following:
                1) DBASS Gene ID
                2) DBASS Gene Name
                3) DBASS Gene Description
                4) Ensembl Gene ID
               with the first line containing column names and all
               subsequent ones containing entries proper. All column
               values, including names from the header as well as any
               empty strings, can be surrounded by pairs of double
               quotes.

               DBASS Gene Name can be either a single name, a
               'name/synonym' pair, or a 'name (synonym)' pair.

               Ensembl Gene ID can be an empty string, indicating an
               unmapped entry.

  Return type: none
  Exceptions : throws on all processing errors
  Caller     : ParseSource in the xref pipeline
  Status     : Stable

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 $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 ) )
  {
    croak 'Need to pass source_id, species_id and files as pairs';
  }
  my $csv = Text::CSV->new()
    || confess 'Failed to initialise CSV parser: ' . Text::CSV->error_diag();
 
  my $filename = @{$files}[0];
 
  my $file_io = $self->get_filehandle($filename);
  if ( !defined($file_io) ) {
    confess "Failed to acquire a file handle for '${filename}'";
  }
 
  if ( ! is_file_header_valid( $csv->header( $file_io ) ) ) {
    confess "Malformed or unexpected header in DBASS file '${filename}'";
  }
 
  my $processed_count = 0;
  my $unmapped_count  = 0;
 
  while ( defined( my $line = $csv->getline( $file_io ) ) ) {
 
    if ( scalar @{ $line } < $EXPECTED_NUMBER_OF_COLUMNS ) {
      confess 'Line ' . (2 + $processed_count + $unmapped_count)
        . " of input file '${filename}' has an incorrect number of columns";
    }
 
    # Do not modify the contents of @{$line}, only the output - hence the /r.
    my ( $dbass_gene_id, $dbass_gene_name, $dbass_full_name, $ensembl_id )
      = map { s{\s+\z}{}rmsx } @{ $line };
 
    # Do not attempt to create unmapped xrefs. Checking truthiness is good
    # enough here because the only non-empty string evaluating as false is
    # not a valid Ensembl stable ID.
    if ( $ensembl_id ) {
 
      # DBASS files list synonyms in two ways: either "FOO (BAR)" (with or
      # without space) or "FOO/BAR". Both forms are relevant to us.
      my ( $first_gene_name, $second_gene_name );
      if ( ( $dbass_gene_name =~ m{
                                    (.*)
                                    \s?\/\s?  # typically no ws here but just in case
                                    (.*)
                                  }msx ) ||
           ( $dbass_gene_name =~ m{
                                    (.*)
                                    \s?  # there are entries both with and without ws
                                    [(] (.*) [)]
                                  }msx ) ) {
        $first_gene_name  = $1;
        $second_gene_name = $2;
      }
      else {
        $first_gene_name = $dbass_gene_name;
        $second_gene_name = undef;
      }
 
      my $label       = $first_gene_name;
      my $synonym     = $second_gene_name;
      my $type        = 'gene';
      my $version     = '1';
 
      my $xref_id =
        $self->get_xref( $dbass_gene_id, $source_id, $species_id, $dbi );
 
      if ( ( ! defined $xref_id ) || ( $xref_id eq q{} ) ) {
        $xref_id = $self->add_xref({
          acc        => $dbass_gene_id,
          version    => $version,
          label      => $label,
          source_id  => $source_id,
          dbi        => $dbi,
          species_id => $species_id,
          info_type  => 'DIRECT'
        });
      }
 
      if ( defined($synonym) ) {
        $self->add_synonym( $xref_id, $synonym, $dbi );
      }
 
      $self->add_direct_xref( $xref_id, $ensembl_id, $type, undef, $dbi );
 
      ++$processed_count;
    }
    else {
      ++$unmapped_count;
    }
 
  } ## end while ( defined( my $line...))
 
  $csv->eof;
  $file_io->close();
 
  if ($verbose) {
    printf( "%d direct xrefs succesfully processed\n", $processed_count );
    printf( "Skipped %d unmapped xrefs\n", $unmapped_count );
  }
 
  return 0;
} ## end sub run

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

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

public map()

XrefParser::DBASSParser::run

public void run()

XrefParser::DBASSParser::is_file_header_valid

public Boolean is_file_header_valid()

XrefParser
DBASSParser
Generated on Wed Oct 2 2024 14:29:00 for ensembl-hive by 1.8.17