None
SWISS::DEs.pm
SWISS::DEs represents the \s-1DE\s0 lines of a UniProt Knowledgebase (Swiss-Prot + TrEMBL) entry as specified in the user manual http://www.expasy.org/sprot/userman.html.
The DEs object basically holds lists of \s-1DE\s0 objects, each of them representing a protein name element. The \*(C`elements\*(C', \*(C`hasFragment\*(C', \*(C`Includes\*(C' and \*(C`Contains\*(C' attributes/methods work as follows :
DE RecName: Full=CAD protein;
DE Short=CAD;
DE AltName: Full=Protein rudimentary;
DE Includes:
DE RecName: Full=Glutamine-dependent carbamoyl-phosphate synthase;
DE EC=6.3.5.5;
DE Includes:
DE RecName: Full=Aspartate carbamoyltransferase;
DE EC=2.1.3.2;
DE Flags: Fragment;
-= Entry::DEs =-
elements (for each DE object, see SWISS::DE.pm documentation) :
toText: "CAD protein", "CAD", "Protein rudimentary"
category: "RecName", "RecName", "AltName"
type: "Full", "Short" "Full"
hasFragment : "Fragment"
Includes : ListBase of DEs (child1, child2)
Contains : empty ListBase
-= child1 =-
elements (for each DE object) :
toText: "Glutamine-dependent carbamoyl-
phosphate synthase", "6.3.5.5"
category: "RecName", "RecName",
type: "Full", "EC"
hasFragment : undef
-= child2 =-
elements (for each DE object) :
toText: "Aspartate carbamoyltransferase", "2.1.3.2"
category: "RecName", "RecName",
type: "Full", "EC"
hasFragment : undef
Note: the old unstructured \s-1DE\s0 format can still be used, and will be parsed the same way into \s-1DE\s0 objects (but without setting their attributes 'category' and 'type'.
DE CAD protein (Protein rudimentary) [Includes: Glutamine-dependent DE carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate DE carbamoyltransferase (EC 2.1.3.2)] (Fragment).
SWISS::ListBase.pm
The (raw) text of the \s-1DE\s0 line (without the '\s-1DE\s0 ' line type prefixes) Array reference to the \s-1SWISS::DE\s0 objects containing the different names for the entry. The first element of the list is the recommended name. Note: use \*(C`elements\*(C' method (inherited from ListBase) to get (and loop through) the array of \s-1DE\s0 objetcs. Each of these is a SWISS::ListBase object whose list contains a SWISS::DEs object for each 'child' of the protein (i.e. peptide or functional domain). See the UniProtKB user manual for an explanation. It is possible to have both Includes and Contains in a single entry: DE RecName: Full=Arginine biosynthesis bifunctional protein argJ; DE Includes: DE RecName: Full=Glutamate N-acetyltransferase; DE EC=2.3.1.35; DE AltName: Full=Ornithine acetyltransferase; DE Short=OATase; DE AltName: Full=Ornithine transacetylase; DE Includes: DE RecName: Full=Amino-acid acetyltransferase; DE EC=2.3.1.1; DE AltName: Full=N-acetylglutamate synthase; DE Short=AGS; DE RecName: Full=Arginine biosynthesis bifunctional protein argJ alpha chain; DE Contains: DE RecName: Full=Arginine biosynthesis bifunctional protein argJ beta chain; Contains 'Fragment' or 'Fragments' (evaluates to true) if the \s-1DE\s0 lines contain the 'Fragment(s)' indication (in 'Flags:' line with the new \s-1DE\s0 line format), otherwise evaluates to false. Compare to the more robust Entry::isFragment which also checks the \s-1FT\s0 lines for a \s-1NON_CONS\s0 or \s-1NON_TER\s0. Returns 1 if the flag 'Precursor' is present (undef if not). Note: only with new \s-1DE\s0 line format.
With the new \s-1DE\s0 line format, each \s-1DE\s0 element can have distinct evidence tags, which are stored in the \s-1DE\s0 object themself (see \s-1SWISS::DE\s0.pm documentation). The evidence tags for the 'Flags' line are stored in the parent DEs object itself. With the old \s-1DE\s0 line format, since the \s-1DE\s0 line did not have a fixed syntax in TrEMBL, it is impossible to reliably assign evidence tags separately to the different elements of the \s-1DE\s0 lines. Therefore, the \s-1DE\s0 line can only be evidence tagged as a whole, and the following methods have their prototype defined in SWISS::BaseClass instead of the direct parent of SWISS::DEs, SWISS::ListBase :
addEvidenceTag deleteEvidenceTags getEvidenceTags getEvidenceTagsString hasEvidenceTag setEvidenceTags
example :
$evidenceTag = $entry->Stars->EV->addEvidence('P', 'DEfix', '-', 'v1.3'); # add global DE evtag if old DE line format, 'Flags' evtag if new format $entry -> DEs -> addEvidenceTag($evidenceTag);