def test5_10_duplicate(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}/B1.fq,{sample_dir}/B2.fq,,
[fusionfusion]
A_tumor,list1
[controlpanel]
list1,pool1
list1,pool2
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test6_06_unformat(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[bam_import]
A_tumor,{sample_dir}/A.Aligned.sortedByCoord.out.bam,{sample_dir}/B.Aligned.sortedByCoord.out.bam
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test6_02_unformat_ok(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
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertFalse(fail)
def test2_04_not_exists(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[bam_tofastq],,,,
A_control,{sample_dir}/X.Aligned.sortedByCoord.out.bam,,,
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def main(args):
###
# set run_conf
run_conf = rc.Run_conf(
sample_conf_file=args.sample_conf_file,
project_root=args.project_root,
gcat_conf_file=args.gcat_conf_file,
)
#run_conf.analysis_type = args.analysis_type
#run_conf.drmaa = False if args.disable_drmaa else True
run_conf.runner = args.runner
run_conf.retry_count = args.retry_count
# disable params
# - args.multiprocess
# - args.param_check
###
# set gcat_conf and task parameter config data
defaut_conf = pkg_resources.resource_filename(
'gcat_workflow', args.analysis_type + '/data/default.ini')
gcat_conf = gc.gcat_conf(conf=run_conf.gcat_conf_file,
default_conf=defaut_conf,
exist_check=not args.ignore_invalid_path)
gcat_conf.software_version_set()
if args.analysis_type == "rna":
import gcat_workflow.rna.sample_conf as sc
import gcat_workflow.rna.configure as configure
elif args.analysis_type == "germline":
import gcat_workflow.germline.sample_conf as sc
import gcat_workflow.germline.configure as configure
elif args.analysis_type == "somatic":
import gcat_workflow.somatic.sample_conf as sc
import gcat_workflow.somatic.configure as configure
sample_conf = sc.Sample_conf(run_conf.sample_conf_file,
exist_check=not args.ignore_invalid_path)
configure.main(gcat_conf=gcat_conf,
run_conf=run_conf,
sample_conf=sample_conf)
def test4_04_duplicate(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[sra_fastq_dump],,,,
tumorA,RUNID123
tumorA,RUNID456
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test5_05_duplicate(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[bam_tofastq],,,,
A_tumor,{sample_dir}/A.Aligned.sortedByCoord.out.bam,,,
[sra_fastq_dump],,,,
A_tumor,RUNID123
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sample_conf = 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
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test3_05_undefine(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """[fastq]
pool1,{sample_dir}/A1.fastq,{sample_dir}/A2.fastq
[controlpanel]
list1,pool100
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test5_08_duplicate(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
[expression]
A_tumor
A_tumor
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
try:
fail = False
sample_conf = sc.Sample_conf(ss_path)
except Exception as e:
print(e)
fail = True
self.assertTrue(fail)
def test1_03_ok(self):
ss_path = self.SAMPLE_DIR + "/" + sys._getframe(
).f_code.co_name + ".csv"
data = """
[bam_tofastq]
A_tumor,{sample_dir}/A.Aligned.sortedByCoord.out.bam
A_control,{sample_dir}/A.Aligned.sortedByCoord.out.bam
pool1,{sample_dir}/A.Aligned.sortedByCoord.out.bam
[fusionfusion]
A_tumor,list1,list2
[controlpanel]
list1,pool1
""".format(sample_dir=self.SAMPLE_DIR)
f = open(ss_path, "w")
f.write(data)
f.close()
sample_conf = sc.Sample_conf(ss_path)
self.assertEqual(sample_conf.fusionfusion, [('A_tumor', 'list1')])
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,,
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_2.fq,,
A_tumor_s,{sample_dir}/A1.fastq
pool1_s,{sample_dir}/B1.fq
pool2_s,{sample_dir}/C1_1.fq;{sample_dir}/C1_2.fq,,,,
[bam_tofastq],,,,
A_control,{sample_dir}/A.Aligned.sortedByCoord.out.bam,,,
[bam_import],,,,
pool3,{sample_dir}/A.Aligned.sortedByCoord.out.bam,,,
pool7,{sample_dir}/B.Aligned.sortedByCoord.out.bam,,,
pool8,{sample_dir}/D.Aligned.sortedByCoord.out.cram,,,
pool9,{sample_dir}/E.Aligned.sortedByCoord.out.cram,,,
[sra_fastq_dump],,,,
pool4,RUNID123456
pool5,RUNID123456,http://dummy.com/data/run.sra
pool6,RUNID123456,{sample_dir}/run.sra
[fusionfusion],,,,
A_tumor,list1,,
A_control,None,,
,,,,
[expression],,,,
A_tumor,,,,
A_tumor_s,,,,
,,,,
[star_fusion],,,,
A_tumor,,,,
[intron_retention],,,,
A_tumor,,,,
[iravnet],,,,
A_tumor,,,,
[juncmut],,,,
A_tumor,,,,
[kallisto],,,,
A_tumor,,,,
[qc],,,,
A_tumor,,,,
A_control,,,,
pool1,,,,
pool2,,,,
pool3,,,,
pool4,,,,
pool5,,,,
pool6,,,,
pool7,,,,
pool8,,,,
pool9,,,,
,,,,
[controlpanel]
list1,pool1,pool2,pool3,pool4,pool5,pool6,pool7,pool8,pool9
""".format(sample_dir=self.SAMPLE_DIR)
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_tumor_s': [[self.SAMPLE_DIR + '/A1.fastq']],
'pool1': [[self.SAMPLE_DIR + '/B1.fq'],
[self.SAMPLE_DIR + '/B2.fq']],
'pool1_s': [[self.SAMPLE_DIR + '/B1.fq']],
'pool2':
[[self.SAMPLE_DIR + '/C1_1.fq', self.SAMPLE_DIR + '/C1_2.fq'],
[self.SAMPLE_DIR + '/C2_1.fq', self.SAMPLE_DIR + '/C2_2.fq']],
'pool2_s':
[[self.SAMPLE_DIR + '/C1_1.fq', self.SAMPLE_DIR + '/C1_2.fq']],
})
self.assertEqual(
sample_conf.fastq_src, {
'A_tumor': [[self.SAMPLE_DIR + '/A1.fastq'],
[self.SAMPLE_DIR + '/A2.fastq']],
'A_tumor_s': [[self.SAMPLE_DIR + '/A1.fastq'], []],
'pool1': [[self.SAMPLE_DIR + '/B1.fq'],
[self.SAMPLE_DIR + '/B2.fq']],
'pool1_s': [[self.SAMPLE_DIR + '/B1.fq'], []],
'pool2':
[[self.SAMPLE_DIR + '/C1_1.fq', self.SAMPLE_DIR + '/C1_2.fq'],
[self.SAMPLE_DIR + '/C2_1.fq', self.SAMPLE_DIR + '/C2_2.fq']],
'pool2_s': [[
self.SAMPLE_DIR + '/C1_1.fq', self.SAMPLE_DIR + '/C1_2.fq'
], []],
})
self.assertEqual(
sample_conf.sra_fastq_dump, {
'pool4': ['RUNID123456', None],
'pool5': ['RUNID123456', "http://dummy.com/data/run.sra"],
'pool6': ['RUNID123456', self.SAMPLE_DIR + '/run.sra']
})
self.assertEqual(sample_conf.bam_tofastq, {
'A_control':
self.SAMPLE_DIR + '/A.Aligned.sortedByCoord.out.bam'
})
self.assertEqual(sample_conf.bam_tofastq_src, {
'A_control':
[self.SAMPLE_DIR + '/A.Aligned.sortedByCoord.out.bam']
})
self.assertEqual(
sample_conf.bam_import, {
'pool3': self.SAMPLE_DIR + '/A.Aligned.sortedByCoord.out.bam',
'pool7': self.SAMPLE_DIR + '/B.Aligned.sortedByCoord.out.bam',
})
self.assertEqual(
sample_conf.bam_import_src, {
'pool3': [
self.SAMPLE_DIR + '/A.Aligned.sortedByCoord.out.bam',
self.SAMPLE_DIR + '/A.Aligned.sortedByCoord.out.bam.bai'
],
'pool7': [
self.SAMPLE_DIR + '/B.Aligned.sortedByCoord.out.bam',
self.SAMPLE_DIR + '/B.Aligned.sortedByCoord.out.bai'
],
})
self.assertEqual(
sample_conf.cram_import, {
'pool8': self.SAMPLE_DIR + '/D.Aligned.sortedByCoord.out.cram',
'pool9': self.SAMPLE_DIR + '/E.Aligned.sortedByCoord.out.cram'
})
self.assertEqual(
sample_conf.cram_import_src, {
'pool8': [
self.SAMPLE_DIR + '/D.Aligned.sortedByCoord.out.cram',
self.SAMPLE_DIR + '/D.Aligned.sortedByCoord.out.cram.crai'
],
'pool9': [
self.SAMPLE_DIR + '/E.Aligned.sortedByCoord.out.cram',
self.SAMPLE_DIR + '/E.Aligned.sortedByCoord.out.crai'
]
})
self.assertEqual(sample_conf.fusionfusion, [('A_tumor', 'list1'),
('A_control', None)])
self.assertEqual(sample_conf.expression, ['A_tumor', 'A_tumor_s'])
self.assertEqual(sample_conf.qc, [
'A_tumor', 'A_control', 'pool1', 'pool2', 'pool3', 'pool4',
'pool5', 'pool6', 'pool7', 'pool8', 'pool9'
])
self.assertEqual(
sample_conf.control_panel, {
'list1': [
'pool1', 'pool2', 'pool3', 'pool4', 'pool5', 'pool6',
'pool7', 'pool8', 'pool9'
]
})
self.assertEqual(sample_conf.star_fusion, ['A_tumor'])
self.assertEqual(sample_conf.ir_count, ['A_tumor'])
self.assertEqual(sample_conf.iravnet, ['A_tumor'])
self.assertEqual(sample_conf.juncmut, ['A_tumor'])
self.assertEqual(sample_conf.kallisto, ['A_tumor'])
