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