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comparison GTranslator.py @ 2:c56b8a6bd02e draft

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author nedias
date Wed, 12 Oct 2016 00:03:46 -0400
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1:3814470e221a 2:c56b8a6bd02e
1 """
2 Translate nucleotide code to polypeptide
3 Because condon table is never change, so in consider of read/exe performance,
4 it is hard-coded, not writen in XML or other format of files, nor store in database
5 TODO: Need to add condon table for RNA
6
7 Author Nedias
8 """
9
10 from Bio.Alphabet import generic_protein
11 from Bio.Seq import Seq
12
13
14 # Nucleotide to Polypeptide mapping
15 def condon_table():
16 c_table = dict()
17
18 c_table["TTT"] = "F"
19 c_table["TTC"] = "F"
20 c_table["TTA"] = "L"
21 c_table["TTG"] = "L"
22 c_table["CTT"] = "L"
23 c_table["CTC"] = "L"
24 c_table["CTA"] = "L"
25 c_table["CTG"] = "L"
26 c_table["ATT"] = "I"
27 c_table["ATC"] = "I"
28 c_table["ATA"] = "I"
29 c_table["ATG"] = "M"
30 c_table["GTT"] = "V"
31 c_table["GTC"] = "V"
32 c_table["GTA"] = "V"
33 c_table["GTG"] = "V"
34 c_table["TCT"] = "S"
35 c_table["TCA"] = "S"
36 c_table["TCC"] = "S"
37 c_table["TCG"] = "S"
38 c_table["CCT"] = "P"
39 c_table["CCC"] = "P"
40 c_table["CCA"] = "P"
41 c_table["CCG"] = "P"
42 c_table["ACT"] = "T"
43 c_table["ACC"] = "T"
44 c_table["ACA"] = "T"
45 c_table["ACG"] = "T"
46 c_table["GCT"] = "A"
47 c_table["GCC"] = "A"
48 c_table["GCA"] = "A"
49 c_table["GCG"] = "A"
50 c_table["TAT"] = "Y"
51 c_table["TAC"] = "Y"
52 c_table["TAA"] = "stop"
53 c_table["TAG"] = "stop"
54 c_table["CAT"] = "H"
55 c_table["CAC"] = "H"
56 c_table["CAA"] = "Q"
57 c_table["CAG"] = "Q"
58 c_table["AAT"] = "N"
59 c_table["AAC"] = "N"
60 c_table["AAA"] = "K"
61 c_table["AAG"] = "K"
62 c_table["GAT"] = "D"
63 c_table["GAC"] = "D"
64 c_table["GAA"] = "E"
65 c_table["GAG"] = "E"
66 c_table["TGT"] = "C"
67 c_table["TGC"] = "C"
68 c_table["TGA"] = "stop"
69 c_table["TGG"] = "W"
70 c_table["CGT"] = "R"
71 c_table["CGC"] = "R"
72 c_table["CGA"] = "R"
73 c_table["CGG"] = "R"
74 c_table["AGT"] = "S"
75 c_table["AGC"] = "S"
76 c_table["AGA"] = "R"
77 c_table["AGG"] = "R"
78 c_table["GGT"] = "G"
79 c_table["GGC"] = "G"
80 c_table["GGA"] = "G"
81 c_table["GGG"] = "G"
82 c_table.update(dict((c_table[i], i) for i in c_table))
83
84 return c_table
85
86
87 # Nucleotide to Polypeptide mapping for complementary sequence
88 def rev_condon_table():
89
90 c_table = dict()
91
92 c_table["AAA"] = "F"
93 c_table["AAG"] = "F"
94 c_table["AAT"] = "L"
95 c_table["AAC"] = "L"
96 c_table["GAA"] = "L"
97 c_table["GAG"] = "L"
98 c_table["GAT"] = "L"
99 c_table["GAC"] = "L"
100 c_table["TAA"] = "I"
101 c_table["TAG"] = "I"
102 c_table["TAT"] = "I"
103 c_table["TAC"] = "M"
104 c_table["CAA"] = "V"
105 c_table["CAG"] = "V"
106 c_table["CAT"] = "V"
107 c_table["CAC"] = "V"
108 c_table["AGA"] = "S"
109 c_table["AGT"] = "S"
110 c_table["AGG"] = "S"
111 c_table["AGC"] = "S"
112 c_table["GGA"] = "P"
113 c_table["GGG"] = "P"
114 c_table["GGT"] = "P"
115 c_table["GGC"] = "P"
116 c_table["TGA"] = "T"
117 c_table["TGG"] = "T"
118 c_table["TGT"] = "T"
119 c_table["TGC"] = "T"
120 c_table["CGA"] = "A"
121 c_table["CGG"] = "A"
122 c_table["CGT"] = "A"
123 c_table["CGC"] = "A"
124 c_table["ATA"] = "Y"
125 c_table["ATG"] = "Y"
126 c_table["ATT"] = "stop"
127 c_table["ATC"] = "stop"
128 c_table["GTA"] = "H"
129 c_table["GTG"] = "H"
130 c_table["GTT"] = "Q"
131 c_table["GTC"] = "Q"
132 c_table["TTA"] = "N"
133 c_table["TTG"] = "N"
134 c_table["TTT"] = "K"
135 c_table["TTC"] = "K"
136 c_table["CTA"] = "D"
137 c_table["CTG"] = "D"
138 c_table["CTT"] = "E"
139 c_table["CTC"] = "E"
140 c_table["ACA"] = "C"
141 c_table["ACG"] = "C"
142 c_table["ACT"] = "stop"
143 c_table["ACC"] = "W"
144 c_table["GCA"] = "R"
145 c_table["GCG"] = "R"
146 c_table["GCT"] = "R"
147 c_table["GCC"] = "R"
148 c_table["TCA"] = "S"
149 c_table["TCG"] = "S"
150 c_table["TCT"] = "R"
151 c_table["TCC"] = "R"
152 c_table["CCA"] = "G"
153 c_table["CCG"] = "G"
154 c_table["CCT"] = "G"
155 c_table["CCC"] = "G"
156 c_table.update(dict((c_table[i], i) for i in c_table))
157
158 return c_table
159
160
161 # Check if the sequence is a multiple of 3
162 # input: Nucleotide sequence in SeqRecords format or string format
163 # output: check result
164 def check_seq(seq):
165
166 if len(seq) % 3 == 0:
167 return True
168 else:
169 return False
170
171
172 # Translate Nucleotide to Polypeptide
173 # input: 1.seq: Nucleotide sequence in SeqRecords format
174 # 2.rev: True if +strand(use normal mapping), False for -strand(use complementary mapping)
175 # return: Polypeptide sequence in Seq format
176 def nucleotide_to_polypeptide(seq, rev):
177
178 poly_seq = ""
179 # If -strand, use complementary mapping
180 if rev:
181 c_table = rev_condon_table()
182 # If +strand, use normal mapping
183 else:
184 c_table = condon_table()
185
186 # If sequence length is a multiple of 3
187 if check_seq(seq):
188 str_seq = str(seq)
189 # Translate every 3 nucleotide acid to one polypeptide
190 for i in xrange(0, len(str_seq) - 3, 3):
191 poly_seq += c_table[str_seq[i:i+3]]
192 return Seq(poly_seq, generic_protein)
193
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