1
2
4 - def __init__(self, name, version, description = ""):
8
9
10
11
13 - def __init__(self, name, accession, description, length):
18
19
20
22 - def __init__(self, name, letters, entries):
26
28 - def __init__(self, full_description, info):
29 self.__dict__.update(info)
30 self.full_description = full_description
31
32
34 - def __init__(self, algorithm, query, database, table, hits,
35 parameters, statistics):
43
45 - def __init__(self, name, description, accession, length,
46 algorithm, hsps = None):
55
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
76 - def __init__(self, length, identical, positives, gaps):
77 self.length = length
78 self.identical = identical
79 self.positives = positives
80 self.gaps = gaps
84 if name == "frac_identical":
85 return float(self.identical) / self.length
86 elif name == "frac_positives":
87 return float(self.positives) / self.length
88 raise AttributeError(name)
89
90
92 - def __init__(self, seq, identical, positives, gaps):
95
97 - def __init__(self, name, seq, location, identical, positives, gaps):
102
103
104 -class HSP(_SeqLength):
105 - def __init__(self,
106 query_seq,
107 homology_seq,
108 subject_seq,
109
110 query_location,
111 subject_location,
112
113 query_name,
114 subject_name,
115
116 algorithm,
117 info,
118 homology_gaps = None,
119 ):
120 assert len(query_seq) == len(homology_seq) == len(subject_seq), \
121 (query_seq, homology_seq, subject_seq)
122 self.algorithm = algorithm
123
124 query_gaps = query_seq.count("-")
125 subject_gaps = subject_seq.count("-")
126 if homology_gaps is None:
127 homology_gaps = query_gaps + subject_gaps
128 self.info = info
129
130 identical = info["identical"]
131
132 positives = info.get("positives", identical)
133
134 _SeqLength.__init__(self, len(query_seq), identical,
135 positives, homology_gaps)
136
137 self.query = HSPSeq(name = query_name,
138 seq = query_seq,
139 location = query_location,
140 identical = identical,
141 positives = positives,
142 gaps = query_gaps)
143
144 self.subject = HSPSeq(name = subject_name,
145 seq = subject_seq,
146 location = subject_location,
147 identical = identical,
148 positives = positives,
149 gaps = subject_gaps)
150 self.homology = HomologySeq(seq = homology_seq,
151 identical = identical,
152 positives = positives,
153 gaps = homology_gaps)
154