Python profile_create_8 Examples

Example #1

File: test_ssw.py Project: jeffdaily/parasail-python

def test1():
    p = parasail.ssw_init("asdf", parasail.blosum62, 1)
    r = parasail.ssw_profile(p, "asdf", 10, 1)

    print(p.s1)
    print(p.s1Len)
    print(r.cigarLen)
    print(r.cigar[0])

    r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
    c = r.cigar
    print(c.len)
    print(c.seq[0])
    print(c.decode)

    p = parasail.profile_create_8("asdf", parasail.blosum62)
    r = parasail.sw_trace_striped_profile_8(p, "asdf", 10, 1)
    c = r.cigar
    print(c.len)
    print(c.seq[0])

    r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
    print(r.query)
    print(r.ref)

Example #2

File: test_ssw.py Project: sabiqali/parasail-python

    def test1(self):
        p = parasail.ssw_init("asdf", parasail.blosum62, 1)
        r = parasail.ssw_profile(p, "asdf", 10, 1)

        print(p.s1)
        print(p.s1Len)
        print(r.cigarLen)
        print(r.cigar[0])

        r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
        c = r.cigar
        print(c.len)
        print(c.seq[0])
        print(c.decode)

        p = parasail.profile_create_8("asdf", parasail.blosum62)
        r = parasail.sw_trace_striped_profile_8(p, "asdf", 10, 1)
        c = r.cigar
        print(c.len)
        print(c.seq[0])

        r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
        print(r.query)
        print(r.ref)

Example #3

    def test(self):
        result = parasail.sw_table("asdf", "asdfasdf", 10, 1,
                                   parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        with self.assertRaises(AttributeError):
            print(result.matches)
        with self.assertRaises(AttributeError):
            print(result.similar)
        with self.assertRaises(AttributeError):
            print(result.length)
        print(result.score_table)

        result = parasail.sw_stats_table("asdf", "asdfasdf", 10, 1,
                                         parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        print(result.matches)
        print(result.similar)
        print(result.length)
        print(result.score_table)
        print(result.matches_table)
        print(result.similar_table)
        print(result.length_table)

        result = parasail.sw_rowcol("asdf", "asdfasdf", 10, 1,
                                    parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        with self.assertRaises(AttributeError):
            print(result.matches)
        with self.assertRaises(AttributeError):
            print(result.similar)
        with self.assertRaises(AttributeError):
            print(result.length)
        print(result.score_row)
        print(result.score_col)

        result = parasail.sw_stats_rowcol("asdf", "asdfasdf", 10, 1,
                                          parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        print(result.matches)
        print(result.similar)
        print(result.length)
        print(result.score_row)
        print(result.score_col)
        print(result.matches_row)
        print(result.matches_col)
        print(result.similar_row)
        print(result.similar_col)
        print(result.length_row)
        print(result.length_col)

        result = parasail.sw("asdf", "asdf", 10, 1, parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        with self.assertRaises(AttributeError):
            print(result.matches)
        with self.assertRaises(AttributeError):
            print(result.similar)
        with self.assertRaises(AttributeError):
            print(result.length)
        with self.assertRaises(AttributeError):
            print(result.score_table)

        result = parasail.sw_stats("asdf", "asdf", 10, 1, parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        print(result.matches)
        print(result.similar)
        print(result.length)

        result = parasail.sw_scan_32("asdf", "asdf", 10, 1, parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        with self.assertRaises(AttributeError):
            print(result.matches)
        with self.assertRaises(AttributeError):
            print(result.similar)
        with self.assertRaises(AttributeError):
            print(result.length)

        result = parasail.sw_scan_16("asdf", "asdf", 10, 1, parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        with self.assertRaises(AttributeError):
            print(result.matches)
        with self.assertRaises(AttributeError):
            print(result.similar)
        with self.assertRaises(AttributeError):
            print(result.length)

        result = parasail.sw_stats_striped_16("asdf", "asdf", 10, 1,
                                              parasail.blosum62)
        print(result)
        print(result.saturated)
        print(result.score)
        print(result.matches)
        print(result.similar)
        print(result.length)

        print(parasail.blosum62.name)
        print(parasail.blosum62.size)
        print(parasail.blosum62.matrix)

        profile = parasail.profile_create_8("asdf", parasail.blosum62)
        profile = parasail.profile_create_8("asdf", parasail.blosum62)
        print(profile)
        print(profile.s1)
        print(profile.matrix)

        result = parasail.sw_striped_profile_8(profile, "asdf", 10, 1)
        print(result)
        print(result.saturated)
        print(result.score)

        profile = parasail.profile_create_sat("asdf", parasail.blosum62)
        print(profile)
        print(profile.s1)
        print(profile.matrix)
        print(dir(profile.matrix))
        print(profile.matrix.min)
        print(profile.matrix.max)
        print(profile.matrix.size)

        result = parasail.sw_striped_profile_sat(profile, "asdf", 10, 1)
        print(result)
        print(result.saturated)
        print(result.score)
        print(type(result.score))

Example #4

File: test_basic.py Project: iiSeymour/parasail-python

def test4():
    profile = parasail.profile_create_8("asdf", parasail.blosum62)
    result = parasail.sw_striped_profile_8(profile, "asdf", 10, 1)
    assert (result.score == 20)
    del result
    del profile

Example #5

File: test_basic.py Project: sabiqali/parasail-python

 def test4(self):
     profile = parasail.profile_create_8("asdf", parasail.blosum62)
     result = parasail.sw_striped_profile_8(profile, "asdf", 10, 1)
     self.assertEqual(result.score, 20)

Example #6

File: test_tables.py Project: jeffdaily/parasail-python

def test():
    result = parasail.sw_table("asdf","asdfasdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length
    print result.score_table

    result = parasail.sw_stats_table("asdf","asdfasdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length
    print result.score_table
    print result.matches_table
    print result.similar_table
    print result.length_table

    result = parasail.sw_rowcol("asdf","asdfasdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length
    print result.score_row
    print result.score_col

    result = parasail.sw_stats_rowcol("asdf","asdfasdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length
    print result.score_row
    print result.score_col
    print result.matches_row
    print result.matches_col
    print result.similar_row
    print result.similar_col
    print result.length_row
    print result.length_col

    result = parasail.sw("asdf","asdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length
    with pytest.raises(AttributeError):
        print result.score_table

    result = parasail.sw_stats("asdf","asdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length

    result = parasail.sw_scan_32("asdf","asdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length

    result = parasail.sw_scan_16("asdf","asdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length

    result = parasail.sw_stats_striped_16("asdf","asdf",10,1,parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length

    print parasail.blosum62.name
    print parasail.blosum62.size
    print parasail.blosum62.matrix

    profile = parasail.profile_create_8("asdf", parasail.blosum62)
    profile = parasail.profile_create_8("asdf", parasail.blosum62)
    print profile
    print profile.s1
    print profile.matrix

    result = parasail.sw_striped_profile_8(profile,"asdf",10,1)
    print result
    print result.saturated
    print result.score

    profile = parasail.profile_create_sat("asdf", parasail.blosum62)
    print profile
    print profile.s1
    print profile.matrix
    print dir(profile.matrix)
    print profile.matrix.min
    print profile.matrix.max
    print profile.matrix.size

    result = parasail.sw_striped_profile_sat(profile,"asdf",10,1)
    print result
    print result.saturated
    print result.score
    print type(result.score)

Example #7

def test():
    result = parasail.sw_table("asdf", "asdfasdf", 10, 1, parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length
    print result.score_table

    result = parasail.sw_stats_table("asdf", "asdfasdf", 10, 1,
                                     parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length
    print result.score_table
    print result.matches_table
    print result.similar_table
    print result.length_table

    result = parasail.sw_rowcol("asdf", "asdfasdf", 10, 1, parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length
    print result.score_row
    print result.score_col

    result = parasail.sw_stats_rowcol("asdf", "asdfasdf", 10, 1,
                                      parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length
    print result.score_row
    print result.score_col
    print result.matches_row
    print result.matches_col
    print result.similar_row
    print result.similar_col
    print result.length_row
    print result.length_col

    result = parasail.sw("asdf", "asdf", 10, 1, parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length
    with pytest.raises(AttributeError):
        print result.score_table

    result = parasail.sw_stats("asdf", "asdf", 10, 1, parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length

    result = parasail.sw_scan_32("asdf", "asdf", 10, 1, parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length

    result = parasail.sw_scan_16("asdf", "asdf", 10, 1, parasail.blosum62)
    print result
    print result.saturated
    print result.score
    with pytest.raises(AttributeError):
        print result.matches
    with pytest.raises(AttributeError):
        print result.similar
    with pytest.raises(AttributeError):
        print result.length

    result = parasail.sw_stats_striped_16("asdf", "asdf", 10, 1,
                                          parasail.blosum62)
    print result
    print result.saturated
    print result.score
    print result.matches
    print result.similar
    print result.length

    print parasail.blosum62.name
    print parasail.blosum62.size
    print parasail.blosum62.matrix

    profile = parasail.profile_create_8("asdf", parasail.blosum62)
    profile = parasail.profile_create_8("asdf", parasail.blosum62)
    print profile
    print profile.s1
    print profile.matrix

    result = parasail.sw_striped_profile_8(profile, "asdf", 10, 1)
    print result
    print result.saturated
    print result.score

    profile = parasail.profile_create_sat("asdf", parasail.blosum62)
    print profile
    print profile.s1
    print profile.matrix
    print dir(profile.matrix)
    print profile.matrix.min
    print profile.matrix.max
    print profile.matrix.size

    result = parasail.sw_striped_profile_sat(profile, "asdf", 10, 1)
    print result
    print result.saturated
    print result.score
    print type(result.score)