pythonlesson/scoring.py at master · Smiley90/pythonlesson · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
def MatchQuality(seq1, seq2):
    '''
    Inputs: seq1 & seq2 are FASTA sequences obtained from genome
sequencing
    Return: Score describing quality of the match based on:
    +1 for each matching basepair
    -1 for each mismatching basepair
    +0 for missing partner/gap
    '''
    matchcounter = 0
    for x in range(len(seq1)):
        seq1char = seq1[x]
        seq2char = seq2[x]
        if seq2char == seq1char:
            if seq1char == '-' and seq2char == '-':
                matchcounter = matchcounter
            else:
                matchcounter = matchcounter + 1
        elif seq2char == '-':
            matchcounter = matchcounter
        elif seq1char == '-':
            matchcounter = matchcounter
        elif x == (len(seq1)+1):
            break
        elif x == (len(seq2)+1):
            break
        else:
            matchcounter = matchcounter - 1

    return matchcounter


def MatchQuality(seq1, seq2):
    '''
    Inputs: seq1 & seq2 are FASTA sequences obtained from genome
sequencing
    Return: Score describing quality of the match based on:
    +1 for each matching basepair
    -1 for each mismatching basepair
    +0 for missing partner/gap
    '''

    bestmatch = 0
    for i in range(abs(len(seq1) - len(seq2))+1):
        matchcounter = 0
        if len(seq1) > len(seq2):
            length = range(len(seq2))
        else:
            length = range(len(seq1))
        for x in length:
            if len(seq1) > len(seq2):
                seq1char = seq1[x+i]
                seq2char = seq2[x]
            elif len(seq2) > len(seq1):
                seq1char = seq1[x]
                seq2char = seq2[x+i]
            else:
                seq1char = seq1[x]
                seq2char = seq2[x]
            if seq2char == seq1char:
                if seq1char == '-' and seq2char == '-':
                    matchcounter = matchcounter
                else:
                    matchcounter = matchcounter + 1
            elif seq2char == '-':
                matchcounter = matchcounter
            elif seq1char == '-':
                matchcounter = matchcounter
            else:
                matchcounter = matchcounter - 1

        if matchcounter > bestmatch:
            bestmatch = matchcounter

            mseq1='-'
            mseq2='-'
            time = 0
            if len(seq1) > len(seq2):
                while time < i:
                    mseq2 += mseq2[0]
                    time += 1
                mseq1 += seq1
                mseq2 += seq2
                time = 0
                while time < (abs(len(seq1) - len(seq2))  - i):
                    mseq2 += mseq2[0]
                    time += 1
            elif len(seq2) > len(seq1):
                while time < i:
                    mseq1 += mseq1[0]
                    time += 1
                mseq1 += seq1
                mseq2 += seq2
                time = 0
                while time < (abs(len(seq1) - len(seq2))  - i):
                    mseq1 += mseq1[0]
                    time += 1

            else:
                mseq1 += seq1
                mseq2 += seq2
            mseq1 += mseq1[0]
            mseq2 += mseq2[0]

    print mseq1
    print mseq2
    return bestmatch