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 ])
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():
arrayNode, arrayList = typeStringsToNodeNamesAndArrays[typeString]
if arrayList.getInherits() != None:
parentArrayNode, parentArrayList = typeStringsToNodeNamesAndArrays[arrayList.getInherits().getType()]
inheritEdges.addDict({ "outNode":parentArrayNode, "inNode":arrayNode })
#We're done
print makeJsonSqgFromSqg(inheritanceGraph)
#Here we dump a dot version of the graph, using the networkX interface.
nxGraph, nxSubgraphs = networkxWrite(inheritanceGraph)
