limitNeighbor = True
if '-force':
limitNeighbor = False
hitRDS = readDataset(hitfile, verbose=True, cache=doCache)
readlen = hitRDS.getReadSize()
normalizationFactor = 1.0
if normalizeBins:
totalCount = len(hitRDS)
normalizationFactor = totalCount / 1000000.
hitDict = hitRDS.getReadsDict(doMulti=True, findallOptimize=True)
hg = Genome(genome)
idb = geneinfoDB(cache=doCache)
gidBins = {}
gidLen = {}
geneinfoDict = idb.getallGeneInfo(genome)
if doFlank:
locusByChromDict = getLocusByChromDict(hg,
upstream=upstreamBp,
downstream=downstreamBp,
useCDS=doCDS,
additionalRegionsDict=acceptDict,
keepSense=True,
adjustToNeighbor=limitNeighbor)
else:
locusByChromDict = getLocusByChromDict(hg,
additionalRegionsDict=acceptDict,
sys.exit(1)
nomatchfilename = ''
genome = sys.argv[1]
infilename = sys.argv[2]
rpkmfilename = sys.argv[3]
outfilename = sys.argv[4]
doCache = False
withSense = False
flankBP = 0
rpkmField = 3
if '-cache' in sys.argv:
doCache = True
cacheGeneDB(genome)
idb = geneinfoDB(cache=True)
print 'cached %s' % genome
else:
idb = geneinfoDB()
if '-sense' in sys.argv:
withSense = True
if '-flank' in sys.argv:
flankBP = int(sys.argv[sys.argv.index('-flank') + 1])
infile = open(infilename)
outfile = open(outfilename, 'w')
geneinfoDict = idb.getallGeneInfo(genome)
posList = []
sys.exit(1)
genome = sys.argv[1]
writeOut = False
if '-outfile' in sys.argv:
writeOut = True
outfilename = sys.argv[sys.argv.index('-outfile') + 1]
restrict = False
if '-restrict' in sys.argv:
restrictfilename = sys.argv[sys.argv.index('-restrict') + 1]
restrict = True
hg = Genome(genome)
idb = geneinfoDB()
GOIDlist = []
for arg in sys.argv:
if 'GO:' in arg:
GOIDlist.append(arg)
print sys.argv
print GOIDlist
firstGeneList = []
for GOID in GOIDlist:
testList = hg.allGIDsbyGOID(GOID)
print 'GOID: %s (%d)' % (GOID, len(testList))
firstGeneList += testList
