def check(self, filename, raises=None): with pysam.TabixFile(filename) as tf: ref = load_and_convert(filename) if raises is None: self.assertEqual(len(list(tf.fetch())), len(ref)) else: self.assertRaises(raises, tf.fetch)
def check(self, filename, raises=None): with pysam.TabixFile(filename) as tf: ref = load_and_convert(filename) if raises is None: self.assertEqual(len(list(tf.fetch())), len(ref)) else: self.assertRaises(raises, tf.fetch)
def setUp(self): self.tabix = pysam.TabixFile(self.filename) self.compare = load_and_convert(self.filename) self.tmpfilename_uncompressed = 'tmp_TestIterators' with gzip.open(self.filename, "rb") as infile, \ open(self.tmpfilename_uncompressed, "wb") as outfile: outfile.write(infile.read())
def setUp(self): self.tabix = pysam.TabixFile(self.filename) self.compare = load_and_convert(self.filename) self.tmpfilename_uncompressed = 'tmp_TestIterators' with gzip.open(self.filename, "rb") as infile, \ open(self.tmpfilename_uncompressed, "wb") as outfile: outfile.write(infile.read())
def setUp(self): self.tabix = pysam.TabixFile(self.filename) self.compare = load_and_convert(self.filename)
def setUp(self): self.compare = load_and_convert(os.path.join(CBCF_DATADIR, self.filename), encode=False)
def setUp(self): self.tabix = pysam.TabixFile(self.filename) self.compare = load_and_convert(self.filename)
def setUp(self): TestVCF.setUp(self) self.compare = load_and_convert(self.filename, encode=False)
def setUp(self): TestVCF.setUp(self) self.tabix = pysam.TabixFile(self.tmpfilename + ".gz") self.compare = load_and_convert(self.filename)
def setUp(self): self.compare = load_and_convert( os.path.join(CBCF_DATADIR, self.filename), encode=False)
def setUp(self): TestVCF.setUp(self) self.vcf = pysam.VCF() self.compare = load_and_convert(self.filename, encode=False)
def setUp(self): TestVCF.setUp(self) self.tabix = pysam.TabixFile(self.tmpfilename + ".gz") self.compare = load_and_convert(self.filename)