def testAffy3Backwards(self):
# tests the old Affymetrix v3 parser
with open(self.affy3, "r") as f:
lines = f.readlines()
record = CelFile.read_v3(lines)
assert(len(record.DatHeader) > 0)
assert(record.intensities.shape == (5, 5))
assert(record.intensities.shape == record.stdevs.shape)
assert(record.intensities.shape == record.npix.shape)
assert(record.ncols == 5)
assert(record.nrows == 5)
def testAffy3Backwards(self):
# tests the old Affymetrix v3 parser
with open(self.affy3, "r") as f:
lines = f.readlines()
record = CelFile.read_v3(lines)
assert (len(record.DatHeader) > 0)
assert (record.intensities.shape == (5, 5))
assert (record.intensities.shape == record.stdevs.shape)
assert (record.intensities.shape == record.npix.shape)
assert (record.ncols == 5)
assert (record.nrows == 5)
##from Bio.Affy import CelFile
##with open("Affy/affy_v4_example.CEL", "rb") as handle:
## c = CelFile.read(handle)
from Bio.Affy import CelFile
with open("Data/GSE58661_RAW/GSM1416528_LUNG3-01.CEL", "rb") as handle:
c = CelFile.read_v3(handle)