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' ] })