def test_subsamp_small_200(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'G5012.3.subset.bam')
clipDb = os.path.join(inDir, 'TestAssembleTrinity', 'clipDb.fasta')
outBam = util.file.mkstempfname('.out.bam')
read_stats = assembly.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=200)
os.unlink(outBam)
self.assertEqual(read_stats, (200, 172, 172, 185, 172, 13))
def test_subsamp_big_500(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'G5012.3.testreads.bam')
clipDb = os.path.join(inDir, 'TestAssembleTrinity', 'clipDb.fasta')
outBam = util.file.mkstempfname('.out.bam')
read_stats = assembly.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=500)
os.unlink(outBam)
self.assertEqual(read_stats, (18710, 16310, 16310, 500, 500, 0))
def test_subsamp_empty(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'empty.bam')
clipDb = os.path.join(inDir, 'TestAssembleTrinity', 'clipDb.fasta')
outBam = util.file.mkstempfname('.out.bam')
read_stats = assembly.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=10)
os.unlink(outBam)
self.assertEqual(read_stats, (0, 0, 0, 0, 0, 0))
def test_subsamp_big_500(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'G5012.3.testreads.bam')
clipDb = os.path.join(inDir, 'TestAssembleTrinity', 'clipDb.fasta')
outBam = util.file.mkstempfname('.out.bam')
read_stats = assembly.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=500)
os.unlink(outBam)
self.assertEqual(read_stats, (18710, 16310, 16310, 500, 500, 0))
def test_subsamp_small_200(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'G5012.3.subset.bam')
clipDb = os.path.join(inDir, 'TestAssembleTrinity', 'clipDb.fasta')
outBam = util.file.mkstempfname('.out.bam')
read_stats = assembly.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=200)
os.unlink(outBam)
self.assertEqual(read_stats, (200, 172, 172, 185, 172, 13))
def test_subsamp_empty(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'empty.bam')
clipDb = os.path.join(inDir, 'TestAssembleTrinity', 'clipDb.fasta')
outBam = util.file.mkstempfname('.out.bam')
read_stats = assembly.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=10)
os.unlink(outBam)
self.assertEqual(read_stats, (0, 0, 0, 0, 0, 0))
def test_subsamp_small_90(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'G5012.3.subset.bam')
clipDb = os.path.join(inDir, 'TestAssembleSpades', 'clipDb.fasta')
outBam = util.file.mkstempfname('.out.bam')
read_stats = assembly.trim_rmdup_subsamp_reads(inBam,
clipDb,
outBam,
n_reads=90)
os.unlink(outBam)
# counts are individual reads
self.assertEqual(read_stats, (200, 172, 172, 90, 90, 0))
