def newPipeline():
checkArgumentMarkerReducer()
m = DnaUtils.readIUPACFile(sys.argv[1])
mapOligos = DnaUtils.readOligosFile(sys.argv[2], m)
# for k in mapOligos:
# for e in mapOligos[k]:
# print(e)
# sys.exit(1)
readSingleFastQFile(sys.argv[4], 10, "log.txt", mapOligos, sys.argv[3])
def newPipeline():
checkArgumentMarkerReducer()
m = DnaUtils.readIUPACFile(sys.argv[1])
mapOligos = DnaUtils.readOligosFile(sys.argv[2], m)
# for k in mapOligos:
# for e in mapOligos[k]:
# print(e)
# sys.exit(1)
readSingleFastQFile(sys.argv[4], 10, "log.txt", mapOligos, sys.argv[3])
def generatePlot():
checkArgumentMarkerReducer()
logger.debug("IUPAC File : " + sys.argv[2])
iupacMap = DnaUtils.readIUPACFile(sys.argv[2])
logger.debug("forward MarkerMap File : " + sys.argv[3])
logger.debug("reverse MarkerMap File : " + sys.argv[4])
forwardMarkerMap = DnaUtils.readOligosFile(sys.argv[3], iupacMap)
reverseMarkerMap = DnaUtils.readOligosFile(sys.argv[4], iupacMap, True)
rAllOutputFileName = sys.argv[6] + ".r.csv"
fAllOutputFileName = sys.argv[6] + ".f.csv"
fAll = {}
rAll = {}
for root, dirs, files in os.walk(sys.argv[5]):
for f1le in files:
filePath = os.path.join(sys.argv[5], f1le)
logger.debug("file : " + filePath)
f, r = DnaUtils.readmarker(filePath, forwardMarkerMap,
reverseMarkerMap, sys.argv[6], False)
mergeMap(rAll, r)
mergeMap(fAll, f)
indexOsPath = filePath.rfind(os.sep)
if indexOsPath == -1:
indexOsPath = 0
else:
indexOsPath += 1
indexOfDot = filePath.rfind(".")
if indexOfDot == -1:
indexOfDot = len(filePath)
rOutputFileName = filePath[indexOsPath:indexOfDot] + ".r.csv"
fOutputFileName = filePath[indexOsPath:indexOfDot] + ".f.csv"
DnaUtils.mapToCsv(r, rOutputFileName)
DnaUtils.mapToCsv(f, fOutputFileName)
DnaUtils.mapToCsv(rAll, rAllOutputFileName)
DnaUtils.mapToCsv(fAll, fAllOutputFileName)
def generatePlot():
checkArgumentMarkerReducer()
logger.debug("IUPAC File : " + sys.argv[2])
iupacMap = DnaUtils.readIUPACFile(sys.argv[2])
logger.debug("forward MarkerMap File : " + sys.argv[3])
logger.debug("reverse MarkerMap File : " + sys.argv[4])
forwardMarkerMap = DnaUtils.readOligosFile(sys.argv[3], iupacMap)
reverseMarkerMap = DnaUtils.readOligosFile(sys.argv[4], iupacMap, True)
rAllOutputFileName = sys.argv[6] + ".r.csv"
fAllOutputFileName = sys.argv[6] + ".f.csv"
fAll = {}
rAll = {}
for root, dirs, files in os.walk(sys.argv[5]):
for f1le in files:
filePath = os.path.join(sys.argv[5], f1le)
logger.debug("file : " + filePath)
f,r = DnaUtils.readmarker(filePath, forwardMarkerMap, reverseMarkerMap, sys.argv[6], False)
mergeMap(rAll, r)
mergeMap(fAll, f)
indexOsPath = filePath.rfind(os.sep)
if indexOsPath == -1:
indexOsPath = 0
else:
indexOsPath += 1
indexOfDot = filePath.rfind(".")
if indexOfDot == -1:
indexOfDot = len(filePath)
rOutputFileName = filePath[indexOsPath:indexOfDot] + ".r.csv"
fOutputFileName = filePath[indexOsPath:indexOfDot] + ".f.csv"
DnaUtils.mapToCsv(r, rOutputFileName)
DnaUtils.mapToCsv(f, fOutputFileName)
DnaUtils.mapToCsv(rAll, rAllOutputFileName)
DnaUtils.mapToCsv(fAll, fAllOutputFileName)