SWISS::FTs(3pm) User Contributed Perl Documentation SWISS::FTs(3pm)Name
SWISS::FTs
Description
SWISS::FTs represents the FT (feature) lines within an SWISS-PROT + TrEMBL entry as specified in the user manual
http://www.expasy.org/sprot/userman.html .
Inherits from
SWISS::ListBase.pm
Attributes
"list"
An array of arrays. Each element is an array containing: a feature key, from position, to position, description, qualifier, FTId and an
evidence tag. Example: ['CHAIN', 25, 126, 'Alpha chain', 'By similarity', '/FTId=PRO_0000023008', '{EC1}']
Methods
Standard methods
new
fromText
toText
sort
perl v5.10.1 2008-05-30 SWISS::FTs(3pm)
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SWISS::DRs(3pm) User Contributed Perl Documentation SWISS::DRs(3pm)Name
SWISS::DRs
Description
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.pm
Attributes
"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']);
perl v5.10.1 2006-01-26 SWISS::DRs(3pm)
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