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def | Initialize (self, config) |
| Initialize the module establish a connection to the database. More...
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def | CloseConnection (self) |
| Close the connection to the database. More...
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def | Protein2GO (self, protein, category=None, manualOnly=False, limitToTerms=None, omitEvidenceCodeND=False, omitEvidenceCode=[]) |
| Get the GO terms that are annotated to a (list of) protein(s). More...
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def | GO2Protein (self, terms, maxDistance=None, minDistance=None, taxon=[], manualOnly=False, useTrembl=False, limitToProteins=None, relationship=False, omitEvidenceCodeND=False, omitEvidenceCode=[]) |
| Get the UniProtKB accession numbers of the proteins that are annotated to GO term(s) or its/their descendants. More...
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def | TermDescendants (self, terms, maxDistance=None, minDistance=None, relationship=False) |
| Get the GO terms that are descendants of the query term(s) in the GO graph. More...
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def | QueryTerms (self, termParts, operand="AND", category=None) |
| Get GO terms where the full name contains certain query strings. More...
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def | GetSignificanceOfInteractionOverlap (self, queryId, setIds) |
| Compute likelihood ratio and p-value for the overlap of interactions annotated to the query id and the set ids. More...
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def | getAllAnnotations (self, category=None, limit=None, taxon=[], manualOnly=False, omitEvidenceCodeND=False, swissProtOnly=False, omitEvidenceCode=[]) |
| Return all protein-GO associations reported in the database. More...
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def | GetRelationshipTypes (self) |
| Get all relationship types that are stored in the database. More...
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def | GetAllLinks (self, relationship=None, category=None) |
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def cls.GODBAccess.CGODBAccess.getAllAnnotations |
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self, |
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category = None , |
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limit = None , |
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taxon = [] , |
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manualOnly = False , |
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omitEvidenceCodeND = False , |
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swissProtOnly = False , |
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omitEvidenceCode = [] |
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) |
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Return all protein-GO associations reported in the database.
@param category Limit results to a certain GO categogy
@param limit MISSING
@param taxos MISSING
@param manualOnly MISSING
@param omitEvidenceCodeND Deprecated, use omitEvidenceCode
If @c True, evidence codes 'ND' (usually
annotate totally uniformatively to the ontology's root) will be
omitted from the result. If @c False, even annotations with evidence
code 'ND' are reported.
@param omitEvidenceCode Omits the provided evidence code(s) from the
query, e.g. IEA or ND. If this parameter is used and not empty, it will
overwrite potentially conflicting information in humanOnly and
omitEvidenceCodeND.
@return A list of all GO annotations, ordered according to GAF2.0
def cls.GODBAccess.CGODBAccess.Protein2GO |
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self, |
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protein, |
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category = None , |
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manualOnly = False , |
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limitToTerms = None , |
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omitEvidenceCodeND = False , |
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omitEvidenceCode = [] |
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) |
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Get the GO terms that are annotated to a (list of) protein(s).
@param protein UniProtKB accession number(s) of the query protein(s).
@param category If not @c None, limit the annotation to certain GO
categories (either 'BP', 'MF', or 'CC').
@param manualOnly Deprecated, use omitEvidenceCode.
If @c True, only associations of protein to GO terms
that have been manually curated will be included, if @c False, all the
information present in the GO database will be used, including
electronic annotations.
@param limitToTerms If a list of GO terms are provided, they will
be used as a filter and only terms that are present in this list
will be returned.
@param omitEvidenceCodeND Deprecated, use omitEvidenceCode.
If @c True, evidence codes 'ND' (usually
annotate totally uniformatively to the ontology's root) will be
omitted from the result. If @c False, even annotations with evidence
code 'ND' are reported.
@param omitEvidenceCode Omits the provided evidence code(s) from the
query, e.g. IEA or ND. If this parameter is used and not empty, it will
overwrite potentially conflicting information in humanOnly and
omitEvidenceCodeND.
@return A @c list of @c dictionaries containing the annotated GO
terms. Keys of the dictionary are: @c gene_symbol, @c association_date,
@c term_category, @c term_name, @c relationship, @c term_id,
@cevidence_code, @c source_db. Returns @c False if there was an error
(issued by @ref common.ErrorHandler).
def cls.GODBAccess.CGODBAccess.QueryTerms |
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self, |
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termParts, |
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operand = "AND" , |
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category = None |
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) |
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Get GO terms where the full name contains certain query strings.
@param termParts The search string(s).
@param operand Either AND or OR. If multiple terms are provided,
this specifies if any (OR) or all of them (AND) should be contained.
@param category GO namespace or all GO namespaces if left to @c None.
@return A list of lists consisting of GO ID, GO name, and category.