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)
def makeSqgFromJsonSqg(jsonSqg):
"""Make sqg object from json-sqg object
"""
#Fn to parse out variables from top level json
def fn(name, defaultObj):
obj = defaultObj
if name in jsonSqg:
obj = jsonSqg[name]
assert isinstance(obj, defaultObj.__class__)
return obj
name = None
if "name" in jsonSqg:
name = int(jsonSqg["name"])
sqg = Sqg(includes=fn("include", []),
name=name,
parents=fn("parents", []),
sharedVariables=fn("sharedVariables", {}))
arrayListTypes = [ arrayListType for arrayListType in jsonSqg.keys() if arrayListType not in \
("name", "include", "parents", "sharedVariables") ]
while len(arrayListTypes) > 0:
arrayListType = arrayListTypes.pop()
jsonArrayList = jsonSqg[arrayListType]
assert isinstance(jsonArrayList, [].__class__)
properties = jsonArrayList[0]
def fn(name):
if name in properties:
return properties[name]
return None
inherits = fn("inherits")
if inherits != None and inherits in arrayListTypes:
arrayListTypes = [ arrayListType ] + arrayListTypes
continue
if len(jsonArrayList) not in (1, 2, 3):
raise RuntimeError("Got an incorrect number of arguments for a json array list: %s %i" % (jsonArrayList, len(jsonArrayList)))
if len(jsonArrayList) in (1, 2): #In memory
arrayList = InMemoryArrayList(type=arrayListType,
inherits=inherits,
sharedVariables=fn("sharedVariables"),
variables=fn("variables"))
if len(jsonArrayList) == 2:
arrays = jsonArrayList[1]
arrayWidth = arrayList.getArrayWidth()
#Now parse in the different arrays
assert len(arrays) % arrayWidth == 0 #Otherwise the length of the array is not divisible by the length of each entry
for j in xrange(0,len(arrays),arrayWidth):
arrayList.addArray(arrays[j:j+arrayWidth])
else: #On disk
arrayList = OnDiskArrayList(file=jsonArrayList[2],
type=arrayListType,
inherits=inherits,
sharedVariables=fn("sharedVariables"),
variables=fn("variables"))
sqg.setArrayList(arrayList)
return sqg
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 ])
"""Creates a sqg representation of the hierarchy of different ArrayLists as a forest with the graphs that define them also represented.
"""
import os
import sys
import json
import networkx as NX
from pysqg.sqg import Sqg
from pysqg.arrayList import InMemoryArrayList
from pysqg.jsonSqg import makeJsonSqgFromSqg
from pysqg.shared import getPysqgIncludeDir
from pysqg.py.networkX import networkxWrite
inheritanceGraph = Sqg(includes=["mixedGraph"])
arrayLists = InMemoryArrayList(type="arrayLists", inherits="node", variables=[ "name", "string", "arrayNames", "string", "arrayTypes", "string" ]) #Nodes representing array list types
sqgs = InMemoryArrayList(type="sqgs", inherits="node", variables=[ "name", "string" ]) #Nodes representing sqg definitions
inheritEdges = InMemoryArrayList(type="inherit", inherits="directedEdge") #Edges showing inheritance between array lists
graphEdges = InMemoryArrayList(type="graph", inherits="directedEdge") #Edges showing which show which sqg defined which array list
#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
