def test_paired_custom_seq_center(self):
inDir = util.file.get_test_input_path(self)
outBam = util.file.mkstempfname('.bam')
outHeader = util.file.mkstempfname('.txt')
sampleSheet = os.path.join(inDir, 'SampleSheet.csv')
runInfo = os.path.join(inDir, 'RunInfo.xml')
fastq = (os.path.join(inDir, 'mebv-48-5_S17_L001_R1_001.fastq.gz'),
os.path.join(inDir, 'mebv-48-5_S17_L001_R2_001.fastq.gz'))
illumina.miseq_fastq_to_bam(outBam,
sampleSheet,
fastq[0],
inFastq2=fastq[1],
runInfo=runInfo,
sequencing_center='CustomSeqCenter')
rgs = list(
tools.samtools.SamtoolsTool().getReadGroups(outBam).values())
self.assertEqual(len(rgs), 1)
rgs = rgs[0]
self.assertEqual(rgs.get('ID'), 'AEF96')
self.assertEqual(rgs.get('PL'), 'illumina')
self.assertEqual(rgs.get('PU'), 'AEF96.1.GGACTCCT-TATCCTCT')
self.assertEqual(rgs.get('LB'), 'mebv.48.5')
self.assertEqual(rgs.get('SM'), 'mebv.48.5')
self.assertEqual(rgs.get('CN'), 'CustomSeqCenter')
self.assertTrue(rgs.get('DT', '').startswith('2015-08-2'))
def test_paired_1(self):
inDir = util.file.get_test_input_path(self)
outBam = util.file.mkstempfname('.bam')
outHeader = util.file.mkstempfname('.txt')
sampleSheet = os.path.join(inDir, 'SampleSheet.csv')
runInfo = os.path.join(inDir, 'RunInfo.xml')
fastq = (os.path.join(inDir, 'mebv-0-1_S5_L001_R1_001.fastq.gz'),
os.path.join(inDir, 'mebv-0-1_S5_L001_R2_001.fastq.gz'))
illumina.miseq_fastq_to_bam(outBam,
sampleSheet,
fastq[0],
inFastq2=fastq[1],
runInfo=runInfo)
rgs = list(
tools.samtools.SamtoolsTool().getReadGroups(outBam).values())
self.assertEqual(len(rgs), 1)
rgs = rgs[0]
self.assertEqual(rgs.get('ID'), 'AEF96')
self.assertEqual(rgs.get('PL'), 'illumina')
self.assertEqual(rgs.get('PU'), 'AEF96.1.CGTACTAG-CTAAGCCT')
self.assertEqual(
rgs.get('LB'),
u'GID-14-E021.ldifficult-value+for_-Sénégalsample_name0.1')
self.assertEqual(rgs.get('SM'), u'GID-14-E021')
self.assertEqual(rgs.get('CN'), 'M04004')
self.assertTrue(rgs.get('DT', '').startswith('2015-08-2'))
def test_paired_custom_seq_center(self):
inDir = util.file.get_test_input_path(self)
outBam = util.file.mkstempfname('.bam')
outHeader = util.file.mkstempfname('.txt')
sampleSheet = os.path.join(inDir, 'SampleSheet.csv')
runInfo = os.path.join(inDir, 'RunInfo.xml')
fastq = (os.path.join(inDir, 'mebv-48-5_S17_L001_R1_001.fastq.gz'),
os.path.join(inDir, 'mebv-48-5_S17_L001_R2_001.fastq.gz'))
illumina.miseq_fastq_to_bam(outBam, sampleSheet, fastq[0], inFastq2=fastq[1], runInfo=runInfo, sequencing_center='CustomSeqCenter')
rgs = list(tools.samtools.SamtoolsTool().getReadGroups(outBam).values())
self.assertEqual(len(rgs), 1)
rgs = rgs[0]
self.assertEqual(rgs.get('ID'), 'AEF96')
self.assertEqual(rgs.get('PL'), 'illumina')
self.assertEqual(rgs.get('PU'), 'AEF96.1.GGACTCCT-TATCCTCT')
self.assertEqual(rgs.get('LB'), 'mebv.48.5')
self.assertEqual(rgs.get('SM'), 'mebv.48.5')
self.assertEqual(rgs.get('CN'), 'CustomSeqCenter')
self.assertTrue(rgs.get('DT','').startswith('2015-08-2'))
def test_paired_1(self):
inDir = util.file.get_test_input_path(self)
outBam = util.file.mkstempfname('.bam')
outHeader = util.file.mkstempfname('.txt')
sampleSheet = os.path.join(inDir, 'SampleSheet.csv')
runInfo = os.path.join(inDir, 'RunInfo.xml')
fastq = (os.path.join(inDir, 'mebv-0-1_S5_L001_R1_001.fastq.gz'),
os.path.join(inDir, 'mebv-0-1_S5_L001_R2_001.fastq.gz'))
illumina.miseq_fastq_to_bam(outBam, sampleSheet, fastq[0], inFastq2=fastq[1], runInfo=runInfo)
rgs = list(tools.samtools.SamtoolsTool().getReadGroups(outBam).values())
self.assertEqual(len(rgs), 1)
rgs = rgs[0]
self.assertEqual(rgs.get('ID'), 'AEF96')
self.assertEqual(rgs.get('PL'), 'illumina')
self.assertEqual(rgs.get('PU'), 'AEF96.1.CGTACTAG-CTAAGCCT')
self.assertEqual(rgs.get('LB'), 'mebv.0.1')
self.assertEqual(rgs.get('SM'), 'mebv.0.1')
self.assertEqual(rgs.get('CN'), 'M04004')
self.assertTrue(rgs.get('DT','').startswith('2015-08-2'))