def readEdgesFromNX(nxGraph, sqg):
for edge in nxGraph.edges():
edgeAttrib = nxGraph[edge[0]][edge[1]]
edgeArrayDict = edgeAttrib.copy()
if "directed" in edgeAttrib:
del edgeArrayDict['directed']
edgeArrayDict["outNode"] = edge[0]
edgeArrayDict["inNode"] = edge[1]
edgeType = 'directedEdge'
else:
edgeArrayDict["node1"] = edge[0]
edgeArrayDict["node2"] = edge[1]
edgeType = 'edge'
if 'type' in edgeAttrib:
edgeType = edgeAttrib['type']
del edgeArrayDict['type']
edgeArrayList = sqg.getArrayList(edgeType)
if edgeArrayList is None:
variables = None
if edgeType not in AbstractArrayList._arrayListTypes:
variables = getSQGVariablesFromNXAttributes(edgeArrayDict)
edgeArrayList = InMemoryArrayList(type=edgeType, variables=variables)
sqg.setArrayList(edgeArrayList)
edgeArrayList.addDict(edgeArrayDict)
def readSubgraphsFromNX(nxGraph, nxSubgraphList, sqg):
for nxSubgraph in nxSubgraphList:
subgraphType = 'subgraph'
edgeTypes = None
subgraphAttrib = nxSubgraph.graph
subgraphArrayDict = subgraphAttrib.copy()
if 'type' in subgraphAttrib:
subgraphType = subgraphAttrib['type']
del subgraphArrayDict['type']
if 'edgeTypes' in subgraphAttrib:
edgeTypes = subgraphAttrib['edgeTypes']
del subgraphArrayDict['edgeTypes']
subgraphArrayDict['nodes'] = nxSubgraph.nodes()
subgraphArrayList = sqg.getArrayList(subgraphType)
if subgraphArrayList is None:
variables, sharedVariables = None, None
if subgraphType not in AbstractArrayList._arrayListTypes:
variables = getSQGVariablesFromNXAttributes(subgraphArrayDict)
if edgeTypes is not None:
sharedVariables = dict()
sharedVariables["edges"] = edgeTypes
subgraphArrayList = InMemoryArrayList(type=subgraphType,
sharedVariables=sharedVariables,
variables=variables)
sqg.setArrayList(subgraphArrayList)
subgraphArrayList.addDict(subgraphArrayDict)
def readNodesFromNX(nxGraph, sqg):
for node in nxGraph.nodes():
nodeType = 'node'
nodeAttrib = nxGraph.node[node]
nodeArrayDict = nodeAttrib.copy()
if 'type' in nodeAttrib:
nodeType = nodeAttrib['type']
del nodeArrayDict['type']
nodeArrayDict['nodeName'] = node
nodeArrayList = sqg.getArrayList(nodeType)
if nodeArrayList is None:
variables = None
if nodeType not in AbstractArrayList._arrayListTypes:
variables = getSQGVariablesFromNXAttributes(nodeArrayDict)
nodeArrayList = InMemoryArrayList(type=nodeType, variables=variables)
sqg.setArrayList(nodeArrayList)
nodeArrayList.addDict(nodeArrayDict)
from pysqg.sqg import Sqg
sqg = Sqg(includes=[ "ungappedOverlapGraph" ], \
sharedVariables={ "Created":"Assemblathon File Format Working Group using Richard Durbin's example", "Date":"24/11/2011"})
from pysqg.arrayList import InMemoryArrayList
nodes = InMemoryArrayList(type="node")
sqg.setArrayList(nodes)
sqg.getArrayList("node")
nodes.getArrayNames()
nodes.getArrayTypes()
_1 = 0
nodes.addArray([ _1 ])
_2 = 1
nodes.addDict({ "nodeName":_2 })
from pysqg.arrayList import OnDiskArrayList
segmentEdges = OnDiskArrayList(file="./segmentEdges", type="multiLabelledSegment")
sqg.setArrayList(segmentEdges)
segmentEdges.getArrayNames()
segmentEdges.getArrayTypes()
aL, aR = 2, 3
nodes.addArray([ aL ])
nodes.addArray([ aR ])
segmentEdges.addDict({ "inNode":aL, "outNode":aR, "length":10, \
"sequence":"acggtcagca", "degree":1 })
b1L, b1R = 4, 5
nodes.addArray([ b1L ])
nodes.addArray([ b1R ])
segmentEdges.addDict({ "inNode":b1L, "outNode":b1R, "length":6, \
"sequence":"catact", "degree":2 })
b2L, b2R = 6, 7
nodes.addArray([ b2L ])
nodes.addArray([ b2R ])
#Add them to the graph
inheritanceGraph.setArrayList(arrayLists)
inheritanceGraph.setArrayList(sqgs)
inheritanceGraph.setArrayList(inheritEdges)
inheritanceGraph.setArrayList(graphEdges)
#Build the nodes and connect the graphs to the array types
typeStringsToNodeNamesAndArrays = {}
i = 0
for file in os.listdir(getPysqgIncludeDir()):
if file[-5:] == ".json":
Sqg(includes=[file[:-5]]) #This ensures the graphs are in memory
graphNode = i
i = i+1
sqgs.addDict({ "nodeName":graphNode, "name":file[:-5] })
#Now iterate through the new array list types
fileHandle = open(os.path.join(getPysqgIncludeDir(), file), 'r')
jsonSqg = json.load(fileHandle)
fileHandle.close()
for arrayListType in jsonSqg.keys():
if arrayListType not in ("name", "include", "parents", "sharedVariables"): #This is very hacky, it would be nice to have a clean way to know which sqg defined which array list.
arrayList = InMemoryArrayList(type=arrayListType)
arrayNode = i
i = i+1
typeStringsToNodeNamesAndArrays[arrayListType] = (arrayNode, arrayList)
arrayLists.addDict({ "nodeName":arrayNode, "name":arrayListType, "arrayNames":" ".join(arrayList.getArrayNames()), "arrayTypes":" ".join(arrayList.getArrayTypes()) })
graphEdges.addDict({ "outNode":graphNode, "inNode":arrayNode })
#Add in the inherits edges
for typeString in typeStringsToNodeNamesAndArrays.keys():
