|
| def | GetRoot (s) |
| | Get the root data node. More...
|
| |
| def | GetAllNodes (s) |
| | Get all data nodes. More...
|
| |
| def | GetAncestors (s, goID, include=True) |
| | Get ancestor nodes for a certain node. More...
|
| |
| def | GetAllAncestors (s, include=True) |
| | Get ancestor nodes for all nodes in the graph. More...
|
| |
| def | GetChildren (s, goID, include=True) |
| | Get child nodes for a certain node. More...
|
| |
| def | IgnoreRelationships (s, is_a=False, regulates=False, part_of=False, positively_regulates=False, negatively_regulates=False) |
| | Do not take into account certain relationships. More...
|
| |
| def | SetCountsFromAC (s, ac) |
| | Populate graph with counts from an annotation corpus. More...
|
| |
| def | UpdateAllNodes (s) |
| | Transfer content of all data nodes to the internal graph. More...
|
| |
| def | ReadGraphML (s, ffn) |
| | Read a graphml-formatted gene ontology from a file. More...
|
| |
| def | WriteGraphML (s, ffn) |
| | Write the graph to a file. More...
|
| |
| def | ReadOBO (s, ffn, ac) |
| |
| def | GetDistance (s, source, target) |
| | Get the shortest distance between two nodes. More...
|
| |
| def | __init__ (s) |
| | Initialize the internal graph implementation. More...
|
| |
| def | UpdateNode (s, goID) |
| | Transfer content of data node to the internal graph. More...
|
| |
| def | ReadOBO (s, ffn) |
| | Read an OBO-formatted gene ontology from file. More...
|
| |
| def | IsPopulated (s) |
| | Has the graph been populated? More...
|
| |
|
| string | gfn = "/home/antonia/Desktop/Test_files/treetest.graphml"; |
| |
| string | goaffn = "/home/antonia/Desktop/Test_files/treetest.goa.tsv"; |
| |
| | g = CGOGraphNetworkX(); |
| |
| | acMF = CAnnotationCorpus("molecular_function"); |
| |
| | acBP = CAnnotationCorpus("biological_process"); |
| |
| | acCC = CAnnotationCorpus("cellular_component"); |
| |
| | gaf = CGAFReader(); |
| |
◆ GetAllAncestors()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.GetAllAncestors |
( |
|
s, |
|
|
|
include = True |
|
) |
| |
Get ancestor nodes for all nodes in the graph.
@param include (@c Bool) Indicates whether to include the start data
node (@c True) or not (@c False).
@return A @c Dictionary. Key is the GO ID, and its value is a @c list
of references to @ref cls.GOGraphNode.CGOGraphNode
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ GetAllNodes()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.GetAllNodes |
( |
|
s | ) |
|
Get all data nodes.
@return A @c List of references to @ref cls.GOGraphNode.CGOGraphNode
instances. By this way, data can be accessed and modified and remains
attached to the graph.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ GetAncestors()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.GetAncestors |
( |
|
s, |
|
|
|
goID, |
|
|
|
include = True |
|
) |
| |
Get ancestor nodes for a certain node.
@param goID (@c String) GO ID, eg. 'GO:0006865'.
@param include (@c Bool) Indicates whether to include the start data
node (@c True) or not (@c False).
@return A @c List of references to @ref cls.GOGraphNode.CGOGraphNode.
This list is empty if @c goID was not found.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ GetChildren()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.GetChildren |
( |
|
s, |
|
|
|
goID, |
|
|
|
include = True |
|
) |
| |
Get child nodes for a certain node.
@param goID (@c String) GO ID, eg. 'GO:0006915'.
@param include (@c Bool) Indicates whether to include the start data
node (@c True) or not (@c False).
@return A @c List of references to @ref cls.GOGraphNode.CGOGraphNode
This list is empty if @c goID was not found.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ GetDistance()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.GetDistance |
( |
|
s, |
|
|
|
srcGOID, |
|
|
|
dstGOID |
|
) |
| |
Get the shortest distance between two nodes.
Notice that the graph is directed and that edges emerge from more
specific nodes to less specific nodes. See the example GO IDs below.
@param srcGOID (@c String) Source GO ID, eg. 'GO:0006860'.
@param dstGOID (@c String) Destination GO ID, eg. 'GO:0008150'.
@return The number of edges of the shortest path from the source to
the destination node. This number equals -1, if any of the two GO
IDs is not present in the graph.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ GetRoot()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.GetRoot |
( |
|
s | ) |
|
Get the root data node.
The root node is the most general term and eventually each node ends
up in the root node when traveling along the graph's edges.
@return @ref cls.GOGraphNode.CGOGraphNode instance of the root.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ IgnoreRelationships()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.IgnoreRelationships |
( |
|
s, |
|
|
|
is_a = False, |
|
|
|
regulates = False, |
|
|
|
part_of = False, |
|
|
|
positively_regulates = False, |
|
|
|
negatively_regulates = False |
|
) |
| |
Do not take into account certain relationships.
@b Removes from the graph the edges marked with the relationships
indicated by the parameters listed below. @b Attention: Then the
graph is saved, these edges will be missing.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ ReadGraphML()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.ReadGraphML |
( |
|
s, |
|
|
|
ffn |
|
) |
| |
Read a graphml-formatted gene ontology from a file.
Loads a graphml-formatted file into this object. The graph represents
the ontology and may have only nodes with @c id and @c name vertex
attributes, but it can in addition be furnished with @c cnt and @c
freq attributes. The latter is a shortcut to avoid reading an
annotation corpus and populating the graph.
@param ffn Full path file name.
@return (@c Bool) @c True, if the graph was read successfully. @c
False, if the file could not be opened.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ ReadOBO()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.ReadOBO |
( |
|
s, |
|
|
|
ffn, |
|
|
|
ac |
|
) |
| |
◆ SetCountsFromAC()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.SetCountsFromAC |
( |
|
s, |
|
|
|
ac |
|
) |
| |
Populate graph with counts from an annotation corpus.
The annotation corpus delivers information how many GO IDs are
associated with proteins. For each GO ID, the number of associated
proteins is added to each of the ancestor nodes. After completion,
the graph is normalized by _Normalize and is ready for semantic
similarity calculations.
@param ac @ref cls.AnnotationCorpus.CAnnotationCorpus instance.
@return (@c Bool) @c False, if the annotation corpus name does not
match the ontology's root name defined by the graph. An error message
is written. @c True, if the graph has been populated successfully.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ UpdateAllNodes()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.UpdateAllNodes |
( |
|
s | ) |
|
◆ WriteGraphML()
| def cls.GOGraphNetworkX.CGOGraphNetworkX.WriteGraphML |
( |
|
s, |
|
|
|
ffn |
|
) |
| |
Write the graph to a file.
Writes the graph to a file using the internal node and edge
attributes. Since data nodes may have changed after reading, a call to
@ref UpdateAllNodes is performed here as an operation common to all
subclasses. Currently, the exactly those attributes listed in @ref
UpdateAllNodes are written to the graph file.
@param ffn Full path file name.
@return (@c Bool) @c True, if the graph was read successfully. @c
False, if the file could not be opened.
Reimplemented from cls.GOGraphBase.CGOGraphBase.
◆ acBP
| cls.GOGraphNetworkX.CGOGraphNetworkX.acBP = CAnnotationCorpus("biological_process"); |
|
static |
◆ acCC
| cls.GOGraphNetworkX.CGOGraphNetworkX.acCC = CAnnotationCorpus("cellular_component"); |
|
static |
◆ acMF
| cls.GOGraphNetworkX.CGOGraphNetworkX.acMF = CAnnotationCorpus("molecular_function"); |
|
static |
◆ gaf
| cls.GOGraphNetworkX.CGOGraphNetworkX.gaf = CGAFReader(); |
|
static |
◆ gfn
| string cls.GOGraphNetworkX.CGOGraphNetworkX.gfn = "/home/antonia/Desktop/Test_files/treetest.graphml"; |
|
static |
◆ goaffn
| string cls.GOGraphNetworkX.CGOGraphNetworkX.goaffn = "/home/antonia/Desktop/Test_files/treetest.goa.tsv"; |
|
static |
The documentation for this class was generated from the following file:
Public Member Functions inherited from cls.GOGraphBase.CGOGraphBase