def mongoDBRead(database, tempFileGenerator=None):
"""Parses an sqg from a database
"""
#Get the core json sqg object
jsonSqg = database.sqg.find_one()
jsonSqg.pop("_id")
#Now add the json array lists
for arrayListProperties in database.arrayLists.find():
arrayListProperties = arrayListProperties
jsonArrayList = [ arrayListProperties, [] ]
type = arrayListProperties["type"]
arrayListProperties.pop("type")
arrayListProperties.pop("_id")
jsonSqg[type] = jsonArrayList
if tempFileGenerator != None:
jsonArrayList.append(tempFileGenerator())
sqg = makeSqgFromJsonSqg(jsonSqg)
#Now fill in the array lists
for arrayListProperties in database.arrayLists.find():
assert "type" in arrayListProperties
type = arrayListProperties["type"]
arrayList = sqg.getArrayList(type)
assert arrayList != None
for array in database.type.find():
arrayList.addDict(array)
return sqg
def main():
vcf = sqgToVcf(makeSqgFromJsonSqg(json.load(sys.stdin)))
file = open(vcf.referenceName, "w")
file.write(vcf.referenceStr())
file.close()
file = open("variants.fa", "w")
file.write(vcf.variantsStr())
file.close()
adjacencyEdges.addDict({ "node1":cR, "node2":dL, "overlap":-1})
adjacencyEdges.addDict({ "node1":dR, "node2":_2, "overlap":0})
for node1, node2, overlap in adjacencyEdges:
print "node1", node1, "node2", node2, "overlap", overlap
mixedSubgraphs = InMemoryArrayList(type="mixedSubgraph")
mixedSubgraphs.getArrayNames()
mixedSubgraphs.getArrayTypes()
mixedSubgraphs.getSharedVariables()
walks = InMemoryArrayList(type="walk", inherits="mixedSubgraph", variables=[ "start", "int", "stop", "int" ], sharedVariables={ "edges":[ "segmentEdge", "adjacencyEdge" ] })
sqg.setArrayList(walks)
walks.getArrayNames()
walks.getArrayTypes()
walks.addDict({ "subgraphName":0, "nodes":[ _1, aL, aR, b1L, b1R, b1L, b1R, cR, cL, b2R, b2L, cL, cR, dL, dR, _2 ], "start":0, "stop":0 })
walks.addDict({ "subgraphName":1, "nodes":[ aL, aR, b1L, b1R, b1L, b1R, cR, cL, b2L, b2R, cL, cR, dL, dR ], "start":3, "stop":10 })
from pysqg.jsonSqg import makeJsonSqgFromSqg
jsonSqg = makeJsonSqgFromSqg(sqg)
print jsonSqg
from pysqg.jsonSqg import makeSqgFromJsonSqg
makeSqgFromJsonSqg(jsonSqg)
makeJsonSqgFromSqg(sqg, putOnDiskArraysInJsonSqg=True)
import os
os.remove("./segmentEdges")
os.remove("./adjacencyEdges")