Chris Mungall > go-perl-0.14 > GO::Parsers::base_parser

Download:
go-perl-0.14.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  10
Open  1
View/Report Bugs
Source   Latest Release: go-perl-0.15

NAME ^

  GO::Parsers::base_parser     - base class for parsers

SYNOPSIS ^

  do not use this class directly; use GO::Parser

DESCRIPTION ^

AUTHOR ^

show_messages

  Usage   -
  Returns -
  Args    -

normalize_files

  Usage   - @files = $parser->normalize_files(@files)
  Returns -
  Args    -

takes a list of filenames/paths, "glob"s them, uncompresses any compressed files and returns the new file list

litemode

  Usage   - $p->litemode(1)
  Returns -
  Args    - bool

when set, parser will only throw the following events:

id|name|is_a|relationship|namespace

(optimisation for fast parsing)

acc2name_h

  Usage   - $n = $p->acc2name_h->{'GO:0003673'}
  Returns - hashref
  Args    - hashref [optional]

gets/sets a hash mapping IDs to names

this will be automatically set by an ontology parser

a non-ontology parser will use this index to verify the parsed data (see $p->acc_not_found($id), below)

acc_not_found

  Usage   - if ($p->acc_not_found($go_id)) { warn("$go_id not known") }
  Returns - bool
  Args    - acc string

uses acc2name_h - if this hash mapping has been created AND the acc is not in the hash, THEN it is considered not found

This is useful for non-ontology parsers (xref_parser, go_assoc_parser) to check whether a referenced ID is actually present in the ontology

note that if acc2name_h has not been created, then accs cannot be considered not-found, and this will always return 0/false

syntax highlighting: