XrefParser::MGIParser Class Reference

Public Member Functions
public	run ()

Detailed Description

Description

A parser class to parse the MGI (official) source,
creating a DIRECT xref between MGI accession and ensembl mouse gene stable id ENSMUSG*

-species = mus_musculus
-species_id = 10090
-data_uri = http://www.informatics.jax.org/downloads/reports/MRK_ENSEMBL.rpt
-file_format = TSV
-columns = [accession symbol name position chrom ens_gene_stableid] ##ignore other columns

Synopsis

my $parser = XrefParser::MGIParser->new($db->dbh);
$parser->run({
  source_id  => 55,
  species_id => 10090,
  files      => ["MRK_ENSEMBL.rpt"],
});

Definition at line 26 of file MGIParser.pm.

Member Function Documentation

run()

public XrefParser::MGIParser::run

(

)

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

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

  Description: Runs the MGIParser
  Return type: 0 on success
  Exceptions : throws on all processing errors
  Caller     : ParseSource in the xref pipeline
 

Code:

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

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