def precomputeRepeatMap(request):
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "SkittleTree.settings")
from SkittleCore import GraphRequestHandler
from DNAStorage import StorageRequestHandler
specimen = request[0]
dbSpecimen = StorageRequestHandler.GetSpecimen(specimen)
chromosomes = StorageRequestHandler.GetRelatedChromosomes(dbSpecimen)
for chromosome in chromosomes:
length = StorageRequestHandler.GetChromosomeLength(specimen, chromosome)
chunks = range(1, length + 1, 2 ** 16)
for targetIndex in range(request[2], len(chunks), request[1]):
start = chunks[targetIndex]
state = makeRequestPacket(specimen, chromosome, start)
print "Computing: ", state.specimen, state.chromosome, state.start
GraphRequestHandler.handleRequest(state)
print "Done computing ", state.specimen, state.chromosome, state.start
def precomputeAnyGraph(request):
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "SkittleTree.settings")
from SkittleCore import GraphRequestHandler
from DNAStorage import StorageRequestHandler
specimen = request[2]
# chromosomes = StorageRequestHandler.GetRelatedChromosomes(specimen)
for chromosome in ['chrY']: #chromosomes:
length = StorageRequestHandler.GetChromosomeLength(specimen, chromosome)
chunks = [1] #range(1, length+1, 2**16)[-7:]
for targetIndex in range(request[1], len(chunks),
request[0]):#this loop divies up the jobs by PID according to modulo nProcessors
start = chunks[targetIndex]
state = makeRequestPacket(specimen, chromosome, start, request[3], request[4])
print "Computing: ", state.specimen, state.chromosome, state.start
GraphRequestHandler.handleRequest(state)
print "Done computing ", state.specimen, state.chromosome, state.start