def test_set_GT_PLOIDY(self):
test_csvobj = csvline.CSVLine()
assert test_csvobj.ploidy == 0
with pytest.raises(SyntaxError) as exec_info:
test_csvobj.set('GT', [])
assert "PLOIDY must be set before calling set GT" in str(
exec_info.value)
with pytest.raises(TypeError) as exec_info:
test_csvobj.set('GT', "value")
assert "GT takes a list as input" in str(exec_info.value)
for ploidy in xrange(1, 4):
test_csvobj.set('PLOIDY', ploidy)
assert test_csvobj.ploidy == ploidy
assert test_csvobj.get('GT') == [csvline.EMPTYCHAR] * ploidy
with pytest.raises(ValueError) as exec_info:
test_csvobj.set('GT', [csvline.EMPTYCHAR] * (ploidy - 1))
assert "GT[] must be of length" in str(exec_info.value)
value = [1] * ploidy
test_csvobj.set('GT', value)
assert test_csvobj.get('GT') == value
test_csvobj.reinit()
assert test_csvobj.get('GT') == csvline.EMPTYCHAR
def test_invalidate(self):
errorString = "Test invalidate"
test_csvobj = csvline.CSVLine()
assert test_csvobj.isValid
test_csvobj.invalidate(errorString)
assert test_csvobj.isValid == False
assert test_csvobj.error == errorString
def test_FilterId(self):
test_csvobj = csvline.CSVLine()
with pytest.raises(TypeError) as exec_info:
test_csvobj.set('FilterId', "value")
assert "FilterId takes a list as input" in str(exec_info.value)
value = [1] * 4
test_csvobj.set('FilterId', value)
assert test_csvobj.get('numFilter') == len(value)
assert test_csvobj.get('FilterId') == value
def test_runChecks(self):
test_csvobj = csvline.CSVLine()
# No SampleId was set
result = test_csvobj.runChecks()
assert result[0] == False
assert "SampleId" in result[1] and "is invalid" in result[1]
assert "Location" in result[1]
assert "End" in result[1]
assert "ALT must be set" in result[1]
test_csvobj.set('SampleId', -1)
result = test_csvobj.runChecks()
assert result[0] == False
assert "SampleId" in result[1] and "is invalid" in result[1]
test_csvobj.set('SampleId', 1)
result = test_csvobj.runChecks()
assert "SampleId" not in result[1]
assert "Location" in result[1] and "is invalid" in result[1]
assert result[0] == False
test_csvobj.set('Location', -1)
result = test_csvobj.runChecks()
assert result[0] == False
assert "Location" in result[1] and "is invalid" in result[1]
test_csvobj.set('Location', 100)
result = test_csvobj.runChecks()
assert "Location" not in result[1]
assert "End" in result[1] and "is invalid" in result[1]
assert result[0] == False
test_csvobj.set('End', -1)
result = test_csvobj.runChecks()
assert result[0] == False
assert "End" in result[1] and "is invalid" in result[1]
test_csvobj.set('End', 1)
result = test_csvobj.runChecks()
assert result[0] == False
assert "End" in result[1] and "< Start" in result[1]
test_csvobj.set('End', 100)
result = test_csvobj.runChecks()
assert "End" not in result[1]
assert "ALT must be set" in result[1]
assert result[0] == False
test_csvobj.set('ALT', ['A'])
result = test_csvobj.runChecks()
assert "Failed" not in result[1]
assert result[0]
def test_ALT(self):
test_csvobj = csvline.CSVLine()
with pytest.raises(TypeError) as exec_info:
test_csvobj.set('ALT', "value")
assert "ALT takes a list as input" in str(exec_info.value)
value = ['A'] * 4
test_csvobj.set('ALT', value)
assert test_csvobj.numALT == len(value)
assert test_csvobj.get('ALT') == value
assert test_csvobj.get('PL') == [csvline.EMPTYCHAR] * ((
(len(value) + 1) * (len(value) + 2)) / 2)
def test_init_versions(self):
num_versions = 1
for version in xrange(1, (num_versions + 2)):
test_csvobj = csvline.CSVLine(version)
if version >= num_versions:
attribute = "invalid"
else:
attribute = test_csvobj.fieldNames[version][0]
with pytest.raises(ValueError) as exec_info:
test_csvobj.set(attribute, "any")
assert "{0} is not a valid attribute".format(attribute) in str(
exec_info.value)
assert test_csvobj.get(attribute) is None
def test_SB(self):
test_csvobj = csvline.CSVLine()
with pytest.raises(TypeError) as exec_info:
test_csvobj.set('SB', "value")
assert "SB takes a list as input" in str(exec_info.value)
with pytest.raises(ValueError) as exec_info:
test_csvobj.set('SB', [csvline.EMPTYCHAR] * (csvline.NUM_SB - 1))
assert "SB must have {0} entries".format(csvline.NUM_SB) in str(
exec_info.value)
value = [1] * csvline.NUM_SB
test_csvobj.set('SB', value)
assert test_csvobj.get('SB') == value
def checkCSV(self, inFile):
"""
Sorts the output that was generated by the Location
Checks if there are more than 1 entries for a sample at the Location
and merges them
"""
# check csv file for global merging
copyfile(inFile, inFile + '.original')
with open(inFile) as f:
csv_reader = csv.reader(f, delimiter=',')
csv_sorted = sorted(csv_reader, key=lambda row: \
int(row[1]), reverse=False)
with open(inFile, 'w') as outFP:
prev_Location = None
csvMap = dict()
for line in csv_sorted:
csv_line = csvline.CSVLine()
csv_line.loadCSV(line)
SId = csv_line.get('SampleId')
Location = csv_line.get('Location')
if Location != prev_Location:
for l in csvMap.values():
outFP.write(l.getCSVLine())
outFP.write('\n')
prev_Location = Location
del csvMap
csvMap = dict()
csvMap[SId] = csv_line
else:
if SId in csvMap.keys():
self.combineCSVs(csvMap[SId], csv_line)
else:
csvMap[SId] = csv_line
for l in csvMap.values():
outFP.write(l.getCSVLine())
outFP.write('\n')
def test_PL(self):
test_csvobj = csvline.CSVLine()
with pytest.raises(TypeError) as exec_info:
test_csvobj.set('PL', "value")
assert "PL takes a list as input" in str(exec_info.value)
with pytest.raises(SyntaxError) as exec_info:
test_csvobj.set('PL', [])
assert "ALT must be set before calling set PL" in str(exec_info.value)
value = ['A'] * 4
test_csvobj.set('ALT', value)
value = [1] * (test_csvobj.numPL - 1)
with pytest.raises(ValueError) as exec_info:
test_csvobj.set('PL', value)
assert "PL[] must be of length" in str(exec_info.value)
value = [1] * test_csvobj.numPL
test_csvobj.set('PL', value)
assert test_csvobj.get('PL') == value
def test_loadCSV(self):
test_csvobj = csvline.CSVLine()
csv_data = "1,100,100,*,A,*,0,*,*,*,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
csv = pycsv.reader(StringIO.StringIO(csv_data), delimiter=',').next()
test_csvobj.loadCSV(csv)
assert test_csvobj.get('SampleId') == '1'
assert test_csvobj.get('Location') == '100'
assert test_csvobj.get('End') == '100'
assert test_csvobj.get('ALT') == ['A']
assert test_csvobj.get('REF') == '*'
assert test_csvobj.get('QUAL') == '*'
assert test_csvobj.get('FilterId') == []
assert test_csvobj.get('BaseQRankSum') == '*'
assert test_csvobj.get('ClippingRankSum') == '*'
assert test_csvobj.get('MQRankSum') == '*'
assert test_csvobj.get('ReadPosRankSum') == '*'
assert test_csvobj.get('DP') == '*'
assert test_csvobj.get('MQ') == '*'
assert test_csvobj.get('MQ0') == '*'
assert test_csvobj.get('DP_FMT') == '*'
assert test_csvobj.get('MIN_DP') == '*'
assert test_csvobj.get('GQ') == '*'
assert test_csvobj.get('SB') == ['*', '*', '*', '*']
assert test_csvobj.get('AD') == ['*', '*']
assert test_csvobj.get('PL') == ['*', '*', '*']
assert test_csvobj.get('AF') == ['*']
assert test_csvobj.get('AN') == '*'
assert test_csvobj.get('AC') == ['*']
assert test_csvobj.get('PLOIDY') == 0
assert test_csvobj.get('GT') == []
assert test_csvobj.get('PS') == '*'
assert test_csvobj.getCSVLine(True) == csv_data
csv_data = "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,0,0,*,*"
csv = pycsv.reader(StringIO.StringIO(csv_data), delimiter=',').next()
test_csvobj.loadCSV(csv)
assert test_csvobj.get('SampleId') == '1'
assert test_csvobj.get('Location') == '100'
assert test_csvobj.get('End') == '100'
assert test_csvobj.get('ALT') == ['A']
assert test_csvobj.get('REF') == 'T'
assert test_csvobj.get('QUAL') == '5.45'
assert test_csvobj.get('FilterId') == ['1', '2']
assert test_csvobj.get('BaseQRankSum') == '35.7'
assert test_csvobj.get('ClippingRankSum') == '5.7'
assert test_csvobj.get('MQRankSum') == '15.7'
assert test_csvobj.get('ReadPosRankSum') == '17.7'
assert test_csvobj.get('DP') == '7'
assert test_csvobj.get('MQ') == '8.5'
assert test_csvobj.get('MQ0') == '9'
assert test_csvobj.get('DP_FMT') == '2'
assert test_csvobj.get('MIN_DP') == '1'
assert test_csvobj.get('GQ') == '10'
assert test_csvobj.get('SB') == ['21', '22', '23', '24']
assert test_csvobj.get('AD') == ['*', '*']
assert test_csvobj.get('PL') == ['*', '*', '*']
assert test_csvobj.get('AF') == ['3.14']
assert test_csvobj.get('AN') == '100'
assert test_csvobj.get('AC') == ['90']
assert test_csvobj.get('PLOIDY') == 0
assert test_csvobj.get('GT') == []
assert test_csvobj.get('PS') == '*'
assert test_csvobj.getCSVLine(True) == csv_data
csv_data = "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,3,70,71,72,*,*"
csv = pycsv.reader(StringIO.StringIO(csv_data), delimiter=',').next()
test_csvobj.loadCSV(csv)
assert test_csvobj.get('SampleId') == '1'
assert test_csvobj.get('Location') == '100'
assert test_csvobj.get('End') == '100'
assert test_csvobj.get('ALT') == ['A']
assert test_csvobj.get('REF') == 'T'
assert test_csvobj.get('QUAL') == '5.45'
assert test_csvobj.get('FilterId') == ['1', '2']
assert test_csvobj.get('BaseQRankSum') == '35.7'
assert test_csvobj.get('ClippingRankSum') == '5.7'
assert test_csvobj.get('MQRankSum') == '15.7'
assert test_csvobj.get('ReadPosRankSum') == '17.7'
assert test_csvobj.get('DP') == '7'
assert test_csvobj.get('MQ') == '8.5'
assert test_csvobj.get('MQ0') == '9'
assert test_csvobj.get('DP_FMT') == '2'
assert test_csvobj.get('MIN_DP') == '1'
assert test_csvobj.get('GQ') == '10'
assert test_csvobj.get('SB') == ['21', '22', '23', '24']
assert test_csvobj.get('AD') == ['25', '26']
assert test_csvobj.get('PL') == ['70', '71', '72']
assert test_csvobj.get('AF') == ['3.14']
assert test_csvobj.get('AN') == '100'
assert test_csvobj.get('AC') == ['90']
assert test_csvobj.get('PLOIDY') == 0
assert test_csvobj.get('GT') == []
assert test_csvobj.get('PS') == '*'
assert test_csvobj.getCSVLine(True) == csv_data
csv_data = "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,3,70,71,72,2,1,2,*"
csv = pycsv.reader(StringIO.StringIO(csv_data), delimiter=',').next()
test_csvobj.loadCSV(csv)
assert test_csvobj.get('SampleId') == '1'
assert test_csvobj.get('Location') == '100'
assert test_csvobj.get('End') == '100'
assert test_csvobj.get('ALT') == ['A']
assert test_csvobj.get('REF') == 'T'
assert test_csvobj.get('QUAL') == '5.45'
assert test_csvobj.get('FilterId') == ['1', '2']
assert test_csvobj.get('BaseQRankSum') == '35.7'
assert test_csvobj.get('ClippingRankSum') == '5.7'
assert test_csvobj.get('MQRankSum') == '15.7'
assert test_csvobj.get('ReadPosRankSum') == '17.7'
assert test_csvobj.get('DP') == '7'
assert test_csvobj.get('MQ') == '8.5'
assert test_csvobj.get('MQ0') == '9'
assert test_csvobj.get('DP_FMT') == '2'
assert test_csvobj.get('MIN_DP') == '1'
assert test_csvobj.get('GQ') == '10'
assert test_csvobj.get('SB') == ['21', '22', '23', '24']
assert test_csvobj.get('AD') == ['25', '26']
assert test_csvobj.get('PL') == ['70', '71', '72']
assert test_csvobj.get('AF') == ['3.14']
assert test_csvobj.get('AN') == '100'
assert test_csvobj.get('AC') == ['90']
assert test_csvobj.get('PLOIDY') == 2
assert test_csvobj.get('GT') == ['1', '2']
assert test_csvobj.get('PS') == '*'
assert test_csvobj.getCSVLine(True) == csv_data
csv_data = "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,3,70,71,72,2,1,2,12345"
csv = pycsv.reader(StringIO.StringIO(csv_data), delimiter=',').next()
test_csvobj.loadCSV(csv)
assert test_csvobj.get('SampleId') == '1'
assert test_csvobj.get('Location') == '100'
assert test_csvobj.get('End') == '100'
assert test_csvobj.get('ALT') == ['A']
assert test_csvobj.get('REF') == 'T'
assert test_csvobj.get('QUAL') == '5.45'
assert test_csvobj.get('FilterId') == ['1', '2']
assert test_csvobj.get('BaseQRankSum') == '35.7'
assert test_csvobj.get('ClippingRankSum') == '5.7'
assert test_csvobj.get('MQRankSum') == '15.7'
assert test_csvobj.get('ReadPosRankSum') == '17.7'
assert test_csvobj.get('DP') == '7'
assert test_csvobj.get('MQ') == '8.5'
assert test_csvobj.get('MQ0') == '9'
assert test_csvobj.get('DP_FMT') == '2'
assert test_csvobj.get('MIN_DP') == '1'
assert test_csvobj.get('GQ') == '10'
assert test_csvobj.get('SB') == ['21', '22', '23', '24']
assert test_csvobj.get('AD') == ['25', '26']
assert test_csvobj.get('PL') == ['70', '71', '72']
assert test_csvobj.get('AF') == ['3.14']
assert test_csvobj.get('AN') == '100'
assert test_csvobj.get('AC') == ['90']
assert test_csvobj.get('PLOIDY') == 2
assert test_csvobj.get('GT') == ['1', '2']
assert test_csvobj.get('PS') == '12345'
assert test_csvobj.getCSVLine(True) == csv_data
def test_getCSVLine(self):
test_csvobj = csvline.CSVLine()
result = test_csvobj.getCSVLine()
assert "failed" in result
# Update to avoid run check failure
test_csvobj.set('SampleId', 1)
test_csvobj.set('Location', 100)
test_csvobj.set('End', 100)
test_csvobj.set('ALT', ['A'])
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,*,A,*,0,*,*,*,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('REF', 'T')
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,*,0,*,*,*,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('QUAL', 5.45)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,0,*,*,*,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('FilterId', [1, 2])
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,*,*,*,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('BaseQRankSum', 35.7)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,*,*,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('ClippingRankSum', 5.7)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,*,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('MQRankSum', 15.7)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,*,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('ReadPosRankSum', 17.7)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,*,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('MQ', 8.5)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,*,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('MQ0', 9)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,0,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('AF', [3.14])
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,*,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('AN', 100)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,0,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('AC', [90])
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,*,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('DP', 7)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,*,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('DP_FMT', 2)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,*,*,*,*,*,*,0,0,*,*"
test_csvobj.set('MIN_DP', 1)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,*,*,*,*,*,0,0,*,*"
test_csvobj.set('GQ', 10)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,*,*,*,*,0,0,*,*"
test_csvobj.set('SB', range(21, 25))
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,0,0,*,*"
test_csvobj.set('AD', range(25, 27))
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,0,*,*"
test_csvobj.set('PL', range(70, 73))
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,3,70,71,72,*,*"
test_csvobj.set('PLOIDY', 2)
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,3,70,71,72,2,*,*,*"
test_csvobj.set('GT', [1, 2])
assert test_csvobj.getCSVLine(
clear=False
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,3,70,71,72,2,1,2,*"
test_csvobj.set('PS', 12345)
assert test_csvobj.getCSVLine(
clear=True
) == "1,100,100,T,A,5.45,2,1,2,35.7,5.7,15.7,17.7,8.5,9,1,3.14,100,1,90,7,2,1,10,21,22,23,24,2,25,26,3,70,71,72,2,1,2,12345"
assert test_csvobj.numALT == 0