XrefParser::HPAParser Class Reference

Public Member Functions
public	run ()
public Boolean	is_file_header_valid ()

Detailed Description

Description

This parser will read and creates direct xrefs from a simple comma-delimited file downloaded from the Human Protein Atlas (HPA) database.
The database contains two types of antibody, their own HPA antibodies and Collaborator antibody (CAB) commercial antibodies.

 data_uri        = http://www.proteinatlas.org/download/xref.php

The columns of the file should be the following:

 1)  Antibody
 2)  Antibody ID
 3)  Ensembl Peptide ID
 4)  Link (URL)

 Antibody,antibody_id,ensembl_peptide_id,link
 CAB000001,1,ENSP00000363822,http://www.proteinatlas.org/ENSG00000169083-AR
 CAB000001,1,ENSP00000379358,http://www.proteinatlas.org/ENSG00000169083-AR

Synopsis

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

Definition at line 34 of file HPAParser.pm.

Member Function Documentation

is_file_header_valid()

public Boolean XrefParser::HPAParser::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 HPA file follows expected
               syntax.
  Return type: boolean
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

run()

public XrefParser::HPAParser::run

(

)

Undocumented method

Code:

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

• ensembl/misc-scripts/xref_mapping/XrefParser/HPAParser.pm