def testGetTumourSamples(self):
mnf = Manifest.Manifest(os.path.join(wdir, 'contrast2.txt'))
ts = mnf.get_tumour_samples()
self.assertTrue(type(ts) == set)
self.assertEqual(['B', 'C'], sorted(list(ts)))
# W/o tumour samples
mnf = Manifest.Manifest(os.path.join(wdir, 'fastqc.txt'))
self.assertEqual(set(), mnf.get_tumour_samples())
def testCanGetFastqcTable(self):
mnf = Manifest.Manifest(os.path.join(wdir, 'mnf.txt'))
self.assertEqual(6, len(
mnf.fastqc)) # mnf.txt has 4 rows with a duplicate fastq pair
self.assertEqual('N1/fastqc/N1_S4_R1_001.fastq.gz.md5',
list(mnf.fastqc['fastq_md5'])[0])
mnf = Manifest.Manifest(os.path.join(wdir, 'fastqc.txt'))
self.assertEqual(2, len(mnf.fastqc))
self.assertEqual('L1/fastqc/R1/reads.fastq.gz.md5',
list(mnf.fastqc['fastq_md5'])[0])
self.assertEqual('L1/fastqc/R2/reads.fastq.gz.md5',
list(mnf.fastqc['fastq_md5'])[1])
def testCanSymlinkBamFiles(self):
shutil.rmtree('N1', ignore_errors=True)
shutil.rmtree('P1', ignore_errors=True)
shutil.rmtree('T1', ignore_errors=True)
shutil.rmtree('T3', ignore_errors=True)
mnf = Manifest.Manifest('manifest_bam.txt')
mnf.symlink_bam()
# Note Output tree is created in cwd
self.assertTrue(os.path.islink('N1/bwa/N1.bam'))
self.assertTrue(os.path.islink('N1/bwa/N1.bam.bai'))
self.assertTrue(os.path.islink('T1/bwa/T1.bam'))
self.assertTrue(os.path.islink('T1/bwa/T1.bam.bai'))
shutil.rmtree('N1', ignore_errors=True)
shutil.rmtree('P1', ignore_errors=True)
shutil.rmtree('T1', ignore_errors=True)
shutil.rmtree('T3', ignore_errors=True)
def __init__(self,
manifest,
freq_file,
count=100,
prefix=None,
debug=False):
self.debug = debug
# Read in the manifest and store it as a dictionary
self.manifest = Manifest(manifest)
# Generate a set of variants specified in the manifest to be associated with disease somehow.
# Specify the frequency file
self.freq_file = freq_file
self.count = int(count)
self.samples = None
self.prefix = prefix
if prefix is None:
self.prefix = "gsim.%s" % count
self.run()
def testFailMultipleBamsToSameSample(self):
shutil.rmtree('N1', ignore_errors=True)
shutil.rmtree('T1', ignore_errors=True)
mnf = Manifest.Manifest('manifest_bam_dup.txt')
with self.assertRaises(errors.InvalidManifestError):
mnf.symlink_bam()
def testCanMatchedManyToMany(self):
mnf = Manifest.Manifest(os.path.join(wdir, 'manyToMany.txt'))
self.assertEqual(4, len(mnf.contrasts))
def testCanGetMatchedNormalContrasts(self):
mnf = Manifest.Manifest(os.path.join(wdir, 'mnf.txt'))
self.assertEqual(1, len(mnf.contrasts))
self.assertEqual('N1', mnf.contrasts['normal_smp'][0])
self.assertEqual('T1', mnf.contrasts['tumour_smp'][0])
def testLibraryNameSameAsSampleName(self):
# Since manifest does not have 'library' we use the sample name as library id.
mnf = Manifest.Manifest(os.path.join(wdir, 'mnf.txt'))
self.assertEqual(list(mnf.df['sample']), list(mnf.df['library']))
def testCanGetLibraries(self):
mnf = Manifest.Manifest(os.path.join(wdir, 'mnf.txt'))
self.assertEqual(3, len(mnf.sample))
def test_tn_pair_can_be_null(self):
mnf = Manifest.Manifest('contrast2.txt')
self.assertEqual(0, len(mnf.contrasts))
def testFailTooManySamplesToOneContrast(self):
with self.assertRaises(errors.InvalidManifestError):
mnf = Manifest.Manifest('contrast.txt')
def testFailOnManifestWithDuplicateFq(self):
with self.assertRaises(errors.InvalidManifestError):
mnf = Manifest.Manifest('invalid.txt')