Python get_sequences Examples

Example #1

File: test_deblurring.py Project: kimgc1983/deblur-1

    def test_get_sequences_error_length(self):
        seqs = [("151_9240;size=170;", "----tagggcaagactccatg----"),
                ("151_6640;size=1068;", "--acggaggcgagatgcgtggt----"),
                ("151_64278;size=200;", "---tactagcaagattcctgg-----")]

        with self.assertRaises(ValueError):
            get_sequences(seqs)

Example #2

File: test_deblurring.py Project: davideflo/deblur

    def test_get_sequences_error_length(self):
        seqs = [
            ("151_9240;size=170;", "----tagggcaagactccatg----"),
            ("151_6640;size=1068;", "--acggaggcgagatgcgtggt----"),
            ("151_64278;size=200;", "---tactagcaagattcctgg-----"),
        ]

        with self.assertRaises(ValueError):
            get_sequences(seqs)

Example #3

File: test_deblurring.py Project: ekopylova/deblur

 def test_get_sequences(self):
     exp_seqs = [
         Sequence("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"),
         Sequence("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"),
         Sequence("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"),
         Sequence("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"),
         Sequence("151_527;size=964;", "---acggaggatgatgcgcggt-----"),
         Sequence("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"),
         Sequence("151_5777;size=305;", "---ggagtgcaagattccaggt-----"),
         Sequence("151_64278;size=200;", "---tactagcaagattcctggt-----"),
         Sequence("151_9240;size=170;", "---tagggcaagactccatggt-----"),
         Sequence("151_41690;size=157;", "---agg-gcgagattcctagtgg----")]
     obs_seqs = get_sequences(self.seqs)
     self.assertEqual(obs_seqs, exp_seqs)

Example #4

File: test_deblurring.py Project: davideflo/deblur

 def test_get_sequences(self):
     exp_seqs = [
         Sequence("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"),
         Sequence("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"),
         Sequence("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"),
         Sequence("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"),
         Sequence("151_527;size=964;", "---acggaggatgatgcgcggt-----"),
         Sequence("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"),
         Sequence("151_5777;size=305;", "---ggagtgcaagattccaggt-----"),
         Sequence("151_64278;size=200;", "---tactagcaagattcctggt-----"),
         Sequence("151_9240;size=170;", "---tagggcaagactccatggt-----"),
         Sequence("151_41690;size=157;", "---agg-gcgagattcctagtgg----"),
     ]
     obs_seqs = get_sequences(self.seqs)
     self.assertEqual(obs_seqs, exp_seqs)

Example #5

File: test_deblurring.py Project: davideflo/deblur

 def test_get_sequences_error_empty(self):
     with self.assertRaises(ValueError):
         get_sequences([])

Example #6

File: test_deblurring.py Project: kimgc1983/deblur-1

 def test_get_sequences_error_empty(self):
     with self.assertRaises(ValueError):
         get_sequences([])

Example #7

File: test_deblurring.py Project: qiyunzhu/deblur

 def test_get_sequences_error_empty(self):
     self.assertIsNone(get_sequences([]))

Example #8

File: test_deblurring.py Project: bingxinhu/deblur

 def test_get_sequences_empty_file(self):
     gen = skbio.read(join(self.test_data_dir, 'seqs_empty.fasta'),
                      format='fasta')
     self.assertEqual(get_sequences(gen), None)