def test6_09_none(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq]
A_tumor,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq
pool1,{sample_dir}/B1.fq,{sample_dir}/B2.fq
[genomon_sv]
A_tumor,None,list1
[controlpanel]
list1,pool1
[readgroup]
A_tumor,{sample_dir}/A.metadata.txt
pool1,{sample_dir}/B.metadata.txt
""".format(sample_dir=self.SAMPLE_DIR, htcall=HT_CALL)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertFalse(fail)
def test3_04_undefine(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[{bam2fq}]
A_control,{sample_dir}/A.markdup.cram
""".format(sample_dir=self.SAMPLE_DIR, bam2fq=BAM_2FQ)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test5_06_unformat(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[{bamimp}]
A_tumor,{sample_dir}/A.markdup.cram,{sample_dir}/B.markdup.cram
""".format(sample_dir=self.SAMPLE_DIR, bamimp=BAM_IMP)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test5_02_unformat(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq],,,,
A_tumor,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq,{sample_dir}/A2.fastq
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test2_05_not_exists(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[{bamimp}],,,,
pool3,{sample_dir}/X.markdup.cram,,,
""".format(sample_dir=self.SAMPLE_DIR, bamimp=BAM_IMP)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test2_06_not_exists(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq]
A_tumor,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq
[readgroup]
A_tumor,{sample_dir}/A1.metadata.txt
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test2_03_not_exists(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq],,,,
A_tumor,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq,,
pool1,{sample_dir}/B1.fq,{sample_dir}/B2.fq,,
pool2,{sample_dir}/C1_1.fq;{sample_dir}/C1_2.fq,{sample_dir}/C2_1.fq;{sample_dir}/C2_3.fq,,
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test3_03_undefine(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq]
A_tumor,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq
[{htcall}]
B_tumor
""".format(sample_dir=self.SAMPLE_DIR, htcall=HT_CALL)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test4_06_duplicate(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq],,,,
pool3,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq,,
[{bam2fq}],,,,
A_tumor,{sample_dir}/A.markdup.cram,,,
[{bamimp}],,,,
pool3,{sample_dir}/B.markdup.cram,,,
""".format(sample_dir=self.SAMPLE_DIR, bam2fq=BAM_2FQ, bamimp=BAM_IMP)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test6_05_none(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq]
A_tumor,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq
[gridss]
A_tumor
[readgroup]
A_tumor,{sample_dir}/A.metadata.txt
""".format(sample_dir=self.SAMPLE_DIR, htcall=HT_CALL)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertFalse(fail)
def test1_01_allinone(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq]
A_tumor,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq
A_tumor2,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq
pool1,{sample_dir}/B1.fq,{sample_dir}/B2.fq
pool2,{sample_dir}/link_C1_1.fq;{sample_dir}/link_C1_2.fq,{sample_dir}/C2_1.fq;{sample_dir}/C2_2.fq
[{bam2fq}]
A_control,{sample_dir}/A.markdup.cram
A_control2,{sample_dir}/link_A.markdup.cram
[{bamimp}]
pool3,{sample_dir}/B.markdup.cram
pool4,{sample_dir}/link_B.markdup.cram
[{htcall}]
A_tumor,A_control
A_control,None
A_control2
[{summary1}]
A_tumor
[{summary2}]
A_tumor
[manta]
A_tumor,A_control
A_control,None
A_control2
[gridss]
A_tumor,A_control
A_control,None
A_control2
[genomon_sv]
A_tumor,A_control,list1
A_tumor2,None,list1
A_control,None
A_control2
[controlpanel]
list1,pool1,pool2,pool3,pool4
[readgroup]
A_tumor,{sample_dir}/A.metadata.txt
A_tumor2,{sample_dir}/A.metadata.txt
pool1,{sample_dir}/B.metadata.txt
pool2,{sample_dir}/C.metadata.txt
A_control,{sample_dir}/A.metadata.txt
A_control2,{sample_dir}/link_A.metadata.txt
""".format(sample_dir=self.SAMPLE_DIR,
bam2fq=BAM_2FQ,
bamimp=BAM_IMP,
htcall=HT_CALL,
summary1=SUMMARY1,
summary2=SUMMARY2)
f = open(ss_path, "w")
f.write(data)
f.close()
sample_conf = sc.Sample_conf(ss_path)
self.assertEqual(
sample_conf.fastq, {
'A_tumor': [[self.SAMPLE_DIR + '/A1.fastq'],
[self.SAMPLE_DIR + '/A2.fastq']],
'A_tumor2': [[self.SAMPLE_DIR + '/A1.fastq'],
[self.SAMPLE_DIR + '/A2.fastq']],
'pool1': [[self.SAMPLE_DIR + '/B1.fq'],
[self.SAMPLE_DIR + '/B2.fq']],
'pool2': [[
self.SAMPLE_DIR + '/link_C1_1.fq',
self.SAMPLE_DIR + '/link_C1_2.fq'
], [
self.SAMPLE_DIR + '/C2_1.fq', self.SAMPLE_DIR + '/C2_2.fq'
]],
})
self.assertEqual(
sample_conf.fastq_src, {
'A_tumor': [[self.SAMPLE_DIR + '/A1.fastq'],
[self.SAMPLE_DIR + '/A2.fastq']],
'A_tumor2': [[self.SAMPLE_DIR + '/A1.fastq'],
[self.SAMPLE_DIR + '/A2.fastq']],
'pool1': [[self.SAMPLE_DIR + '/B1.fq'],
[self.SAMPLE_DIR + '/B2.fq']],
'pool2': [[
self.SAMPLE_DIR + '/link_C1_1.fq', self.SAMPLE_DIR +
'/C1_1.fq', self.SAMPLE_DIR + '/link_C1_2.fq',
self.SAMPLE_DIR + '/C1_2.fq'
], [
self.SAMPLE_DIR + '/C2_1.fq', self.SAMPLE_DIR + '/C2_2.fq'
]],
})
self.assertEqual(
sample_conf.bam_tofastq, {
'A_control': self.SAMPLE_DIR + '/A.markdup.cram',
'A_control2': self.SAMPLE_DIR + '/link_A.markdup.cram'
})
self.assertEqual(
sample_conf.bam_tofastq_src, {
'A_control': [self.SAMPLE_DIR + '/A.markdup.cram'],
'A_control2': [
self.SAMPLE_DIR + '/link_A.markdup.cram',
self.SAMPLE_DIR + '/A.markdup.cram'
]
})
self.assertEqual(
sample_conf.bam_import, {
'pool3': self.SAMPLE_DIR + '/B.markdup.cram',
'pool4': self.SAMPLE_DIR + '/link_B.markdup.cram'
})
self.assertEqual(
sample_conf.bam_import_src, {
'pool3': [
self.SAMPLE_DIR + '/B.markdup.cram',
self.SAMPLE_DIR + '/B.markdup.crai'
],
'pool4': [
self.SAMPLE_DIR + '/link_B.markdup.cram',
self.SAMPLE_DIR + '/link_B.markdup.crai', self.SAMPLE_DIR +
'/B.markdup.cram', self.SAMPLE_DIR + '/B.markdup.crai'
]
})
self.assertEqual(sample_conf.mutect_call, [('A_tumor', 'A_control'),
('A_control', None),
('A_control2', None)])
self.assertEqual(sample_conf.manta, [('A_tumor', 'A_control'),
('A_control', None),
('A_control2', None)])
self.assertEqual(sample_conf.gridss, [('A_tumor', 'A_control'),
('A_control', None),
('A_control2', None)])
self.assertEqual(sample_conf.wgs_metrics, ['A_tumor'])
self.assertEqual(sample_conf.multiple_metrics, ['A_tumor'])
self.assertEqual(sample_conf.genomon_sv,
[('A_tumor', 'A_control', 'list1'),
('A_tumor2', None, 'list1'),
('A_control', None, None),
('A_control2', None, None)])
self.assertEqual(sample_conf.control_panel,
{'list1': ['pool1', 'pool2', 'pool3', 'pool4']})
self.assertEqual(
sample_conf.readgroup, {
'A_tumor': self.SAMPLE_DIR + '/A.metadata.txt',
'A_tumor2': self.SAMPLE_DIR + '/A.metadata.txt',
'pool1': self.SAMPLE_DIR + '/B.metadata.txt',
'pool2': self.SAMPLE_DIR + '/C.metadata.txt',
'A_control': self.SAMPLE_DIR + '/A.metadata.txt',
'A_control2': self.SAMPLE_DIR + '/link_A.metadata.txt'
})
self.assertEqual(
sample_conf.readgroup_src, {
'A_tumor': [self.SAMPLE_DIR + '/A.metadata.txt'],
'A_tumor2': [self.SAMPLE_DIR + '/A.metadata.txt'],
'pool1': [self.SAMPLE_DIR + '/B.metadata.txt'],
'pool2': [self.SAMPLE_DIR + '/C.metadata.txt'],
'A_control': [self.SAMPLE_DIR + '/A.metadata.txt'],
'A_control2': [
self.SAMPLE_DIR + '/link_A.metadata.txt',
self.SAMPLE_DIR + '/A.metadata.txt'
]
})
