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GO::Parsers::base_parser.3pm

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