Exemplos de write_unmapped_reads em Python

Exemplo n.º 1

    def test_unmapped(self):
        reads = [("A:B:C", ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"), (None, None))]
        expected_reads = []
        expected_unmapped1 = """\
@A:B:C name1
bases1
+
qual1
"""
        expected_unmapped2 = """\
@A:B:C name2
bases2
+
qual2
"""
        unmapped1 = StringIO()
        unmapped2 = StringIO()

        filtered_reads = list(write_unmapped_reads(reads, unmapped1,
                                                   unmapped2))

        self.assertEqual(expected_reads, filtered_reads)
        self.assertEqual(expected_unmapped1, unmapped1.getvalue())
        self.assertEqual(expected_unmapped2, unmapped2.getvalue())

Exemplo n.º 2

Arquivo: test_fastq_g2p.py Projeto: cfe-lab/MiCall

    def test_unmapped(self):
        reads = [("A:B:C",
                  ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"),
                  (None, None))]
        expected_reads = []
        expected_unmapped1 = """\
@A:B:C name1
bases1
+
qual1
"""
        expected_unmapped2 = """\
@A:B:C name2
bases2
+
qual2
"""
        unmapped1 = StringIO()
        unmapped2 = StringIO()

        filtered_reads = list(write_unmapped_reads(reads, unmapped1, unmapped2))

        self.assertEqual(expected_reads, filtered_reads)
        self.assertEqual(expected_unmapped1, unmapped1.getvalue())
        self.assertEqual(expected_unmapped2, unmapped2.getvalue())

Exemplo n.º 3

    def test_no_files(self):
        """ Don't write the files, but still do the filtering. """
        reads = [("A:B:C", ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"), ("ref", "seq")),
                 ("A:B:D", ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"), (None, None))]
        expected_reads = [("ref", "seq")]
        unmapped1 = None
        unmapped2 = None

        filtered_reads = list(write_unmapped_reads(reads, unmapped1,
                                                   unmapped2))

        self.assertEqual(expected_reads, filtered_reads)

Exemplo n.º 4

    def test_mapped(self):
        reads = [("A:B:C", ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"), ("ref", "seq"))]
        expected_reads = [("ref", "seq")]
        expected_unmapped1 = ""
        expected_unmapped2 = ""
        unmapped1 = StringIO()
        unmapped2 = StringIO()

        filtered_reads = list(write_unmapped_reads(reads, unmapped1,
                                                   unmapped2))

        self.assertEqual(expected_reads, filtered_reads)
        self.assertEqual(expected_unmapped1, unmapped1.getvalue())
        self.assertEqual(expected_unmapped2, unmapped2.getvalue())

Exemplo n.º 5

Arquivo: test_fastq_g2p.py Projeto: cfe-lab/MiCall

    def test_mapped(self):
        reads = [("A:B:C",
                  ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"),
                  ("ref", "seq"))]
        expected_reads = [("ref", "seq")]
        expected_unmapped1 = ""
        expected_unmapped2 = ""
        unmapped1 = StringIO()
        unmapped2 = StringIO()

        filtered_reads = list(write_unmapped_reads(reads, unmapped1, unmapped2))

        self.assertEqual(expected_reads, filtered_reads)
        self.assertEqual(expected_unmapped1, unmapped1.getvalue())
        self.assertEqual(expected_unmapped2, unmapped2.getvalue())

Exemplo n.º 6

Arquivo: test_fastq_g2p.py Projeto: cfe-lab/MiCall

    def test_no_files(self):
        """ Don't write the files, but still do the filtering. """
        reads = [("A:B:C",
                  ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"),
                  ("ref", "seq")),
                 ("A:B:D",
                  ("name1", "bases1", "qual1"),
                  ("name2", "bases2", "qual2"),
                  (None, None))]
        expected_reads = [("ref", "seq")]
        unmapped1 = None
        unmapped2 = None

        filtered_reads = list(write_unmapped_reads(reads, unmapped1, unmapped2))

        self.assertEqual(expected_reads, filtered_reads)