Functional similarity computation using a database connection. More...
Inheritance diagram for cls.FunctionalSimilarity.CFunctionalSimilarity:
Collaboration diagram for cls.FunctionalSimilarity.CFunctionalSimilarity:
Public Member Functions | |
| def | __init__ (s) |
| def | GetGOIDsBulk (s, spLst) |
| Get GO terms for a list of proteins/gene IDs. More... | |
| def | Initialize (s, paths, ns, graphByFileName="", initDB=True) |
| Initialize object. More... | |
| def | InitDB (s, paths) |
| Initialize and set up a database connection. More... | |
| def | Close (s) |
| Close the database connection. More... | |
 Public Member Functions inherited from cls.FunctionalSimilarity.CFunctionalSimilarityBase | |
| def | ComputePWSSMatrix (s, sp1, sp2) |
| Compute pairwise semantic similarity matrix for a pair of proteins. More... | |
| def | ComputePWGO (s, go1, go2) |
| Compute pairwise semantic similarity for a pair of GOTerms. More... | |
| def | Initialize (s, paths, ns, graphByFileName="") |
| Initialize module. More... | |
| def | SetSimMeasure (s, measure) |
| Choose computational model for semantic similarity. More... | |
| def | SetManual (s, only) |
| Select manual filtering of GO annotations. More... | |
| def | SetNDRemoval (s, flag) |
| Remove annotations to ND. More... | |
| def | GetIC (s, goID) |
| Get information content of a go term ID. More... | |
| def | SimAvg (s, sp1, sp2) |
| Average similarity. More... | |
| def | SimMax (s, sp1, sp2) |
| Maximum similarity. More... | |
| def | SimRCAvgMax (s, sp1, sp2) |
| Maximum row/column averaged maxima. More... | |
| def | SimBMA (s, sp1, sp2) |
| Best match average. More... | |
| def | SimBMA2 (s, sp1, sp2) |
| Best match average averaged. More... | |
Detailed Description
Functional similarity computation using a database connection.
Constructor & Destructor Documentation
◆ __init__()
| def cls.FunctionalSimilarity.CFunctionalSimilarity.__init__ | ( | s | ) |
Reimplemented from cls.FunctionalSimilarity.CFunctionalSimilarityBase.
Member Function Documentation
◆ Close()
| def cls.FunctionalSimilarity.CFunctionalSimilarity.Close | ( | s | ) |
Close the database connection.
◆ GetGOIDsBulk()
| def cls.FunctionalSimilarity.CFunctionalSimilarity.GetGOIDsBulk | ( | s, | |
| spLst | |||
| ) |
Get GO terms for a list of proteins/gene IDs.
This method queries the GO database. Be aware that this is much slower
than reading the annotation corpus. This method however provides a
suitable interface as it allows to query for multiple genes/proteins
within an ontology.
@param spLst @c List of gene/protein identifier @c Strings native to
GO annotation corpus.
@return @c Dict. Key, native GO annotation corpus gene/protein ID;
value, @c List of GO term IDs associated with key.
◆ InitDB()
| def cls.FunctionalSimilarity.CFunctionalSimilarity.InitDB | ( | s, | |
| paths | |||
| ) |
Initialize and set up a database connection.
@param paths @c CPaths object.
@return @c True, success; @c False, error connecting to database.
◆ Initialize()
| def cls.FunctionalSimilarity.CFunctionalSimilarity.Initialize | ( | s, | |
| paths, | |||
| ns, | |||
graphByFileName = "", |
|||
initDB = True |
|||
| ) |
Initialize object.
See CFunctionalSimilarityBase.
@param initDB If set to @c True, the database connection will also be
set up. This is default, therefore set to @c False if this shall be
omitted.
The documentation for this class was generated from the following file:
