Chris Mungall > go-db-perl-0.01 > GO::Handlers::godb

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Source   Latest Release: go-db-perl-0.04

NAME ^

  GO::Handlers::godb     - Stores parse XML in GO DB

SYNOPSIS ^

  my $handler = GO::Handler::godb->new;  
  my $apph = GO::AppHandle->new([-d=>"go_load"]);
  $handler->apph($apph);
  my $parser = GO::Parser->new;  
  $parser->handler($handler);
  $parser->parse($file);

DESCRIPTION ^

This module is for loading GO/OBO data into a GO Database; it handles ontologies AND associations

The input for this module is the XML events generated by one of the GO::Parser modules

This XML is transformed into "prestore" XML using GO::Handlers::godb_prestore which is part of the go_perl library - this prestore XML matches the GODB schema, which means a generic XML->DB mapping can be used.

the DBIx::DBStag module is used for storing the godb-prestore in the database

SEE ALSO ^

load-go-into-db.pl

optimize_by_dtype

  Usage   - $handler->optimize_by_dtype('go_assoc', $append);
  Returns -
  Args    - format str, bool [optional]

Optimizes DBIx::DBStag loading based on datatype

Certain tables will be cached by unique key

If $append is false, assumes you are loading some files for the first time, and there is no need to do a SELECT/UPDATE on certain tables - see code for details

If you are re-loading files, set $append=1

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