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SWISS::DRs.3pm
Langue: en
Version: 2006-01-26 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
Name
SWISS::DRsDescription
SWISS::DRs represents the DR (database crossreference) lines within an SWISS-PROT + TrEMBL entry as specified in the user manual http://www.expasy.org/sprot/userman.html .Inherits from
SWISS::ListBase.pmAttributes
- "list"
- An array of arrays. Each element is an array (Database_identifier, primary_key, secondary_key[,further elements]).
Methods
Standard methods
- new
- fromText
- toText
- sort
Reading methods
- emblacs
- Returns a list of all EMBL accession numbers. These are the primary keys of EMBL crossreferences.
- pids [$dropVersion]
- Returns a list of all PIDs. These are the secondary keys of EMBL crossreferences.
ATTENTION: The EMBL protein identifiers introduced in 1999 are of the form xxxxx.yy, e.g. CAA33128.1 If $dropVersion is set, the version number (.yy) will be dropped from each PID.
Example:
If the EMBL DR line is
DR EMBL; L37685; AAC41668.1; -.
pids(1) will only return AAC41668, NOT AAC41668.1
Writing methods
- deleteUnlessEvidenceCategories $evidenceCategories, @patterns
- Like del, but deletes an item only if the item has no evidence tags, or if the evidence tags are not in one of the categories given in $evidenceCategories.
Example:
$entry->DRs->deleteUnlessEvidenceCategories('CA', 'FlyBase')
will only delete Flybase DR lines which do not have the evidence category 'A' or 'C'.
Filter functions
- dbName($dbTargetName)
- True if the first element of a DR line (the DB name) matches $dbTargetName. $dbTargetName has to match in full, not only a partial match.
- notDbName($dbTargetName)
- True if the first element of a DR line (the DB name) does NOT macht $dbTargetName.
** lines (SWISS-PROT internal format)
Each DR line may be followed by a ** line like** DR PROSITE; PS12345; XXX_PAT; FALSE_POS_1 These will be stored internally as DR lines with the DB identifier '_HIDDEN_'. Therefore adding a ** PROSITE line is done as: $entry->DRs->add(['_HIDDEN_', 'PS12345', 'XXX_PAT', 'FALSE_POS_1']);
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