Exemplo n.º 1
0
 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)
Exemplo n.º 2
0
 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)
Exemplo n.º 3
0
    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())
Exemplo n.º 4
0
    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())
Exemplo n.º 5
0
    def setUp(self):

        self.tabix = pysam.TabixFile(self.filename)
        self.compare = load_and_convert(self.filename)
Exemplo n.º 6
0
 def setUp(self):
     self.compare = load_and_convert(os.path.join(CBCF_DATADIR,
                                                  self.filename),
                                     encode=False)
Exemplo n.º 7
0
    def setUp(self):

        self.tabix = pysam.TabixFile(self.filename)
        self.compare = load_and_convert(self.filename)
Exemplo n.º 8
0
 def setUp(self):
     TestVCF.setUp(self)
     self.compare = load_and_convert(self.filename, encode=False)
Exemplo n.º 9
0
    def setUp(self):

        TestVCF.setUp(self)

        self.tabix = pysam.TabixFile(self.tmpfilename + ".gz")
        self.compare = load_and_convert(self.filename)
Exemplo n.º 10
0
 def setUp(self):
     self.compare = load_and_convert(
         os.path.join(CBCF_DATADIR, self.filename),
         encode=False)
Exemplo n.º 11
0
    def setUp(self):

        TestVCF.setUp(self)

        self.vcf = pysam.VCF()
        self.compare = load_and_convert(self.filename, encode=False)
Exemplo n.º 12
0
    def setUp(self):

        TestVCF.setUp(self)

        self.tabix = pysam.TabixFile(self.tmpfilename + ".gz")
        self.compare = load_and_convert(self.filename)