SWISS::DRs (3pm)

SWISS::DRs

SWISS::DRs represents the \s-1DR\s0 (database crossreference) lines within an SWISS-PROT + TrEMBL entry as specified in the user manual http://www.expasy.org/sprot/userman.html .

SWISS::ListBase.pm

An array of arrays. Each element is an array (Database_identifier, primary_key, secondary_key[,further elements]).

Standard methods

new

fromText

toText

sort

Reading methods

emblacs

Returns a list of all \s-1EMBL\s0 accession numbers. These are the primary keys of \s-1EMBL\s0 crossreferences.

pids [$dropVersion]

Returns a list of all PIDs. These are the secondary keys of \s-1EMBL\s0 crossreferences. \s-1ATTENTION:\s0 The \s-1EMBL\s0 protein identifiers introduced in 1999 are of the form xxxxx.yy, e.g. \s-1CAA33128\s0.1 If $dropVersion is set, the version number (.yy) will be dropped from each \s-1PID\s0. Example: If the \s-1EMBL\s0 \s-1DR\s0 line is \s-1DR\s0 \s-1EMBL\s0; L37685; \s-1AAC41668\s0.1; -. pids\|(1) will only return \s-1AAC41668\s0, \s-1NOT\s0 \s-1AAC41668\s0.1

Writing methods

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('\s-1CA\s0', 'FlyBase') will only delete Flybase \s-1DR\s0 lines which do not have the evidence category 'A' or 'C'.

Filter functions

dbName($dbTargetName)

True if the first element of a \s-1DR\s0 line (the \s-1DB\s0 name) matches $dbTargetName. $dbTargetName has to match in full, not only a partial match.

notDbName($dbTargetName)

True if the first element of a \s-1DR\s0 line (the \s-1DB\s0 name) does \s-1NOT\s0 macht $dbTargetName.

** lines (SWISS-PROT internal format)

Each \s-1DR\s0 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']);