probe2seq[probe_id] = probe_seq
coord[(int(probe_coor_x), int(probe_coor_y))] = probe_id
probeSequenceTabFile.close()
return probe2seq, coord
celFilePath = sys.argv[1]
celFileName = os.path.basename(celFilePath)
outFilePath = sys.argv[2]
probeSequenceTabFilePath = sys.argv[3]
probeSequenceTabColIndices = [int(x) for x in sys.argv[4].split("/")]
modelProbesFilePath = sys.argv[5]
cel = MyCEL()
norm = Normalize()
if os.path.exists(outFilePath):
print "Already processed %s" % outFilePath
else:
print "Reading annotations"
probe2seq, coord2probe = getMetadata(probeSequenceTabFilePath,
probeSequenceTabColIndices)
print "Reading " + celFilePath
probeIntensity = cel.read_cel(celFilePath, coord2probe)
modelProbes = None
if os.path.exists(modelProbesFilePath):
print "Reading model probes file"
probe2seq[probe_id] = probe_seq
coord[(int(probe_coor_x), int(probe_coor_y))] = probe_id
probeSequenceTabFile.close()
return probe2seq, coord
celFilePath = sys.argv[1]
celFileName = os.path.basename(celFilePath)
outFilePath = sys.argv[2]
probeSequenceTabFilePath = sys.argv[3]
probeSequenceTabColIndices = [int(x) for x in sys.argv[4].split("/")]
modelProbesFilePath = sys.argv[5]
cel = MyCEL()
norm = Normalize()
if os.path.exists(outFilePath):
print "Already processed %s" % outFilePath
else:
print "Reading annotations"
probe2seq, coord2probe = getMetadata(probeSequenceTabFilePath, probeSequenceTabColIndices)
print "Reading " + celFilePath
probeIntensity = cel.read_cel(celFilePath, coord2probe)
modelProbes = None
if os.path.exists(modelProbesFilePath):
print "Reading model probes file"
modelProbes = utilities.readVectorFromFile(modelProbesFilePath)
import glob,os,sys,time,posix import utilities from mycel import MyCEL celFilePath = sys.argv[1] cel = MyCEL() print cel.read_platform(celFilePath)
