Esempio n. 1
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 def test_simple_parse(self):
     """Make sure that we can parse all primersearch files.
     """
     for file in self.test_files:
         h = open(file, "r")
         PrimerSearch.read(h)
         h.close()
Esempio n. 2
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 def test_simple_parse(self):
     """Make sure that we can parse all primersearch files.
     """
     for file in self.test_files:
         h = open(file, "r")
         PrimerSearch.read(h)
         h.close()
Esempio n. 3
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    def test_in_depth_normal_parse(self):
        """Make sure the output from a simple primersearch file is correct."""
        file = self.test_files[0]
        with open(file) as handle:
            amp_info = PrimerSearch.read(handle)

        self.assertEqual(len(amp_info.amplifiers), 1)
        self.assertIn("Test", amp_info.amplifiers)
        self.assertEqual(len(amp_info.amplifiers["Test"]), 1)

        self.assertEqual(amp_info.amplifiers["Test"][0].length, 218)
        self.assertEqual(
            amp_info.amplifiers["Test"][0].hit_info, "AC074298 AC074298 \n"
            "\tTelomere associated sequence for Arabidopsis thaliana "
            "TEL1N from chromosome I, complete sequence.\n"
            "\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 "
            "with 0 mismatches\n"
            "\tTCACATTCCCAAATGTAGATCG hits reverse strand at "
            "[114] with 0 mismatches")
Esempio n. 4
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    def test_in_depth_normal_parse(self):
        """Make sure the output from a simple primersearch file is correct."""
        file = self.test_files[0]
        h = open(file, "r")
        amp_info = PrimerSearch.read(h)
        h.close()

        self.assertEqual(len(amp_info.amplifiers), 1)
        self.assertIn("Test", amp_info.amplifiers)
        self.assertEqual(len(amp_info.amplifiers["Test"]), 1)

        self.assertEqual(amp_info.amplifiers["Test"][0].length, 218)
        self.assertEqual(amp_info.amplifiers["Test"][0].hit_info,
                         "AC074298 AC074298 \n"
                         "\tTelomere associated sequence for Arabidopsis thaliana "
                         "TEL1N from chromosome I, complete sequence.\n"
                         "\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 "
                         "with 0 mismatches\n"
                         "\tTCACATTCCCAAATGTAGATCG hits reverse strand at "
                         "[114] with 0 mismatches")
Esempio n. 5
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    def test_in_depth_normal_parse(self):
        """Make sure the output from a simple primersearch file is correct.
        """
        file = self.test_files[0]
        h = open(file, "r")
        amp_info = PrimerSearch.read(h)
        h.close()

        assert len(amp_info.amplifiers.keys()) == 1
        assert "Test" in amp_info.amplifiers.keys()
        assert len(amp_info.amplifiers["Test"]) == 1

        assert amp_info.amplifiers["Test"][0].length == 218
        assert amp_info.amplifiers["Test"][0].hit_info == \
          "AC074298 AC074298 \n" + \
          "\tTelomere associated sequence for Arabidopsis thaliana " + \
          "TEL1N from chromosome I, complete sequence.\n" + \
          "\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 with " + \
          "0 mismatches\n" + \
          "\tTCACATTCCCAAATGTAGATCG hits reverse strand at [114] with " + \
          "0 mismatches"
Esempio n. 6
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 def test_simple_parse(self):
     """Make sure that we can parse all primersearch files."""
     for file in self.test_files:
         with open(file) as handle:
             PrimerSearch.read(handle)