Python AlignInfo.print_info_content示例

示例#1

文件： test_align.py 项目： fredricj/biopython

    def test_read_write_clustal(self):
        """Test the base alignment stuff."""
        path = os.path.join(os.getcwd(), "Clustalw", "opuntia.aln")
        alignment = AlignIO.read(path,
                                 "clustal",
                                 alphabet=Alphabet.Gapped(
                                     IUPAC.unambiguous_dna))
        self.assertEqual(len(alignment), 7)
        seq_record = alignment[0]
        self.assertEqual(seq_record.description,
                         "gi|6273285|gb|AF191659.1|AF191")
        self.assertEqual(
            seq_record.seq,
            Seq("TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA"
                ))
        seq_record = alignment[1]
        self.assertEqual(seq_record.description,
                         "gi|6273284|gb|AF191658.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA"
        )
        seq_record = alignment[2]
        self.assertEqual(seq_record.description,
                         "gi|6273287|gb|AF191661.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA"
        )
        seq_record = alignment[3]
        self.assertEqual(seq_record.description,
                         "gi|6273286|gb|AF191660.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA"
        )
        seq_record = alignment[4]
        self.assertEqual(seq_record.description,
                         "gi|6273290|gb|AF191664.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA"
        )
        seq_record = alignment[5]
        self.assertEqual(seq_record.description,
                         "gi|6273289|gb|AF191663.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA"
        )
        seq_record = alignment[6]
        self.assertEqual(seq_record.description,
                         "gi|6273291|gb|AF191665.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA"
        )
        self.assertEqual(alignment.get_alignment_length(), 156)
        align_info = AlignInfo.SummaryInfo(alignment)
        consensus = align_info.dumb_consensus()
        self.assertIsInstance(consensus, Seq)
        self.assertEqual(
            consensus,
            "TATACATTAAAGXAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTXCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA"
        )
        dictionary = align_info.replacement_dictionary(["N"])
        self.assertEqual(len(dictionary), 16)
        self.assertAlmostEqual(dictionary[("A", "A")], 1395.0, places=1)
        self.assertAlmostEqual(dictionary[("A", "C")], 3.0, places=1)
        self.assertAlmostEqual(dictionary[("A", "G")], 13.0, places=1)
        self.assertAlmostEqual(dictionary[("A", "T")], 6.0, places=1)
        self.assertAlmostEqual(dictionary[("C", "A")], 3.0, places=1)
        self.assertAlmostEqual(dictionary[("C", "C")], 271.0, places=1)
        self.assertAlmostEqual(dictionary[("C", "G")], 0, places=1)
        self.assertAlmostEqual(dictionary[("C", "T")], 16.0, places=1)
        self.assertAlmostEqual(dictionary[("G", "A")], 5.0, places=1)
        self.assertAlmostEqual(dictionary[("G", "C")], 0, places=1)
        self.assertAlmostEqual(dictionary[("G", "G")], 480.0, places=1)
        self.assertAlmostEqual(dictionary[("G", "T")], 0, places=1)
        self.assertAlmostEqual(dictionary[("T", "A")], 6.0, places=1)
        self.assertAlmostEqual(dictionary[("T", "C")], 12.0, places=1)
        self.assertAlmostEqual(dictionary[("T", "G")], 0, places=1)
        self.assertAlmostEqual(dictionary[("T", "T")], 874.0, places=1)
        matrix = align_info.pos_specific_score_matrix(consensus, ["N"])
        self.assertEqual(
            str(matrix), """\
    A   C   G   T
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  1.0 0.0 0.0 6.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
X  4.0 0.0 3.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
C  0.0 7.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
C  0.0 7.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 4.0
A  4.0 0.0 0.0 0.0
T  0.0 0.0 0.0 3.0
A  3.0 0.0 0.0 0.0
T  0.0 0.0 0.0 1.0
A  1.0 0.0 0.0 0.0
T  0.0 0.0 0.0 1.0
A  1.0 0.0 0.0 0.0
T  0.0 0.0 0.0 1.0
A  1.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
C  1.0 6.0 0.0 0.0
A  6.0 0.0 0.0 1.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
X  0.0 3.0 0.0 4.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 2.0 0.0 5.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
T  0.0 1.0 0.0 6.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
T  0.0 0.0 0.0 7.0
G  1.0 0.0 6.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
""")

        matrix = align_info.pos_specific_score_matrix(chars_to_ignore=["N"])
        self.assertEqual(
            str(matrix), """\
    A   C   G   T
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  1.0 0.0 0.0 6.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
X  4.0 0.0 3.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
C  0.0 7.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
C  0.0 7.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 4.0
A  4.0 0.0 0.0 0.0
T  0.0 0.0 0.0 3.0
A  3.0 0.0 0.0 0.0
T  0.0 0.0 0.0 1.0
A  1.0 0.0 0.0 0.0
T  0.0 0.0 0.0 1.0
A  1.0 0.0 0.0 0.0
T  0.0 0.0 0.0 1.0
A  1.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
C  1.0 6.0 0.0 0.0
A  6.0 0.0 0.0 1.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
X  0.0 3.0 0.0 4.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 2.0 0.0 5.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
T  0.0 1.0 0.0 6.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
T  0.0 0.0 0.0 7.0
G  1.0 0.0 6.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
""")

        second_seq = alignment[1].seq
        matrix = align_info.pos_specific_score_matrix(second_seq, ["N"])
        self.assertEqual(
            str(matrix), """\
    A   C   G   T
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  1.0 0.0 0.0 6.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  4.0 0.0 3.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
C  0.0 7.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
G  0.0 0.0 7.0 0.0
C  0.0 7.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 4.0
A  4.0 0.0 0.0 0.0
-  0.0 0.0 0.0 3.0
-  3.0 0.0 0.0 0.0
-  0.0 0.0 0.0 1.0
-  1.0 0.0 0.0 0.0
-  0.0 0.0 0.0 1.0
-  1.0 0.0 0.0 0.0
-  0.0 0.0 0.0 1.0
-  1.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
C  1.0 6.0 0.0 0.0
A  6.0 0.0 0.0 1.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
T  0.0 3.0 0.0 4.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
C  0.0 2.0 0.0 5.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
C  0.0 7.0 0.0 0.0
T  0.0 1.0 0.0 6.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
T  0.0 0.0 0.0 7.0
G  1.0 0.0 6.0 0.0
T  0.0 0.0 0.0 7.0
A  7.0 0.0 0.0 0.0
C  0.0 7.0 0.0 0.0
C  0.0 7.0 0.0 0.0
A  7.0 0.0 0.0 0.0
G  0.0 0.0 7.0 0.0
A  7.0 0.0 0.0 0.0
""")
        value = align_info.information_content(5, 50, chars_to_ignore=["N"])
        self.assertAlmostEqual(value, 88.42, places=2)
        value = align_info.information_content(chars_to_ignore=["N"])
        self.assertAlmostEqual(value, 287.55, places=2)
        e_freq = {"G": 0.25, "C": 0.25, "A": 0.25, "T": 0.25}
        e_freq_table = FreqTable.FreqTable(e_freq, FreqTable.FREQ,
                                           IUPAC.unambiguous_dna)
        value = align_info.information_content(e_freq_table=e_freq_table,
                                               chars_to_ignore=["N"])
        self.assertAlmostEqual(value, 287.55, places=2)
        self.assertEqual(align_info.get_column(1), "AAAAAAA")
        self.assertAlmostEqual(align_info.ic_vector[1], 2.00, places=2)
        self.assertEqual(align_info.get_column(7), "TTTATTT")
        self.assertAlmostEqual(align_info.ic_vector[7], 1.41, places=2)
        handle = StringIO()
        AlignInfo.print_info_content(align_info, fout=handle)
        self.assertEqual(
            handle.getvalue(), """\
0 T 2.000
1 A 2.000
2 T 2.000
3 A 2.000
4 C 2.000
5 A 2.000
6 T 2.000
7 T 1.408
8 A 2.000
9 A 2.000
10 A 2.000
11 G 2.000
12 A 1.015
13 A 2.000
14 G 2.000
15 G 2.000
16 G 2.000
17 G 2.000
18 G 2.000
19 A 2.000
20 T 2.000
21 G 2.000
22 C 2.000
23 G 2.000
24 G 2.000
25 A 2.000
26 T 2.000
27 A 2.000
28 A 2.000
29 A 2.000
30 T 2.000
31 G 2.000
32 G 2.000
33 A 2.000
34 A 2.000
35 A 2.000
36 G 2.000
37 G 2.000
38 C 2.000
39 G 2.000
40 A 2.000
41 A 2.000
42 A 2.000
43 G 2.000
44 A 2.000
45 A 2.000
46 A 2.000
47 G 2.000
48 A 2.000
49 A 2.000
50 T 2.000
51 A 2.000
52 T 2.000
53 A 2.000
54 T 2.000
55 A 2.000
56 - 0.682
57 - 0.682
58 - 0.333
59 - 0.333
60 - -0.115
61 - -0.115
62 - -0.115
63 - -0.115
64 - -0.115
65 - -0.115
66 A 2.000
67 T 2.000
68 A 2.000
69 T 2.000
70 A 2.000
71 T 2.000
72 T 2.000
73 T 2.000
74 C 1.408
75 A 1.408
76 A 2.000
77 A 2.000
78 T 2.000
79 T 2.000
80 T 1.015
81 C 2.000
82 C 2.000
83 T 2.000
84 T 2.000
85 A 2.000
86 T 2.000
87 A 2.000
88 T 2.000
89 A 2.000
90 C 1.137
91 C 2.000
92 C 2.000
93 A 2.000
94 A 2.000
95 A 2.000
96 T 2.000
97 A 2.000
98 T 2.000
99 A 2.000
100 A 2.000
101 A 2.000
102 A 2.000
103 A 2.000
104 T 2.000
105 A 2.000
106 T 2.000
107 C 2.000
108 T 2.000
109 A 2.000
110 A 2.000
111 T 2.000
112 A 2.000
113 A 2.000
114 A 2.000
115 T 2.000
116 T 2.000
117 A 2.000
118 G 2.000
119 A 2.000
120 T 2.000
121 G 2.000
122 A 2.000
123 A 2.000
124 T 2.000
125 A 2.000
126 T 2.000
127 C 2.000
128 A 2.000
129 A 2.000
130 A 2.000
131 G 2.000
132 A 2.000
133 A 2.000
134 T 2.000
135 C 2.000
136 C 1.408
137 A 2.000
138 T 2.000
139 T 2.000
140 G 2.000
141 A 2.000
142 T 2.000
143 T 2.000
144 T 2.000
145 A 2.000
146 G 2.000
147 T 2.000
148 G 1.408
149 T 2.000
150 A 2.000
151 C 2.000
152 C 2.000
153 A 2.000
154 G 2.000
155 A 2.000
""")

示例#2

文件： test_align.py 项目： Nizy/biopython

          'A' : 0.25,
          'T' : 0.25}

e_freq_table = FreqTable.FreqTable(e_freq, FreqTable.FREQ,
                                   IUPAC.unambiguous_dna)

print 'relative information:', align_info.information_content(
                                   e_freq_table = e_freq_table,
                                   chars_to_ignore = ['N'])

print 'Column 1:', align_info.get_column(1)
print 'IC for column 1:', align_info.ic_vector[1]
print 'Column 7:', align_info.get_column(7)
print 'IC for column 7:', align_info.ic_vector[7]
print 'test print_info_content'
AlignInfo.print_info_content(align_info)
print "testing reading and writing fasta format..."

to_parse = os.path.join(os.curdir, 'Quality', 'example.fasta')

alignment = AlignIO.read(open(to_parse), "fasta",
                         alphabet = Alphabet.Gapped(IUPAC.ambiguous_dna))

# test the base alignment stuff
print 'all_seqs...'
for seq_record in alignment:
    print 'description:', seq_record.description
    print 'seq:', repr(seq_record.seq)

print 'length:', alignment.get_alignment_length()
align_info = AlignInfo.SummaryInfo(alignment)

示例#3

文件： test_align.py 项目： thorbenwiese/bachelorarbeit_wiese

print('relative information content')
e_freq = {'G': 0.25, 'C': 0.25, 'A': 0.25, 'T': 0.25}

e_freq_table = FreqTable.FreqTable(e_freq, FreqTable.FREQ,
                                   IUPAC.unambiguous_dna)

print('relative information: %0.2f' % align_info.information_content(
    e_freq_table=e_freq_table, chars_to_ignore=['N']))

print('Column 1: %s' % align_info.get_column(1))
print('IC for column 1: %0.2f' % align_info.ic_vector[1])
print('Column 7: %s' % align_info.get_column(7))
print('IC for column 7: %0.2f' % align_info.ic_vector[7])
print('test print_info_content')
AlignInfo.print_info_content(align_info)
print("testing reading and writing fasta format...")

to_parse = os.path.join(os.curdir, 'Quality', 'example.fasta')

alignment = AlignIO.read(to_parse,
                         "fasta",
                         alphabet=Alphabet.Gapped(IUPAC.ambiguous_dna))

# test the base alignment stuff
print('all_seqs...')
for seq_record in alignment:
    print('description: %s' % seq_record.description)
    print('seq: %r' % seq_record.seq)

print('length: %i' % alignment.get_alignment_length())