def setUpClass(cls):
platform = 'in_drop_v2'
# cls.bamfile = LOCAL_OUTPUT % platform + '_bamfile.bam'
# cls.annotation = LOCAL_OUTPUT % platform + '_annotations.gtf'
# S3.download(SAMFILE % platform, cls.bamfile, recursive=False)
# S3.download(INDEX + 'annotations.gtf', cls.annotation, recursive=False)
cls.bamfile = os.path.expanduser('~/Downloads/mm_test_short.bam')
cls.annotation = os.path.expanduser('~/Downloads/annotations.gtf')
cls.summary = os.path.expanduser('~/Downloads/mm_test_summary.txt')
cls.total_input_reads = 12242659
cls.translator = gtf.GeneIntervals(cls.annotation, 10000)
def test_construct_translator(self):
translator = gtf.GeneIntervals(self.annotation)
print(len(translator._chromosomes_to_genes))
def test_construct_translator(self):
translator = gtf.GeneIntervals(self.annotation)
self.assertIsNotNone(translator)
def test_translate(self):
translator = gtf.GeneIntervals(self.annotation)
# chr19 HAVANA gene 60951 71626 . - . gene_id "ENSG00000282458.1"; gene_type "transcribed_processed_pseudogene"; gene_status "KNOWN"; gene_name "WASH5P"; level 2; havana_gene "OTTHUMG00000180466.8";
gene_id = translator.translate("chr19", "-", 60951)
self.assertEqual(gene_id, 282458)
def setUp(cls):
cls.test_id = str(uuid.uuid4())
cls.path_temp = os.path.join(os.environ["TMPDIR"], "seqc-test",
str(uuid.uuid4()))
cls.annotation = os.path.join(dataset_local.index, "annotations.gtf")
cls.translator = gtf.GeneIntervals(cls.annotation, 10000)