EvryRNA / BruteSmORF

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b4022c59 1 parent 2828b9c8

alter gen codes

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...@@ -3,10 +3,10 @@ BruteSmORF ...@@ -3,10 +3,10 @@ BruteSmORF
3 3
4 4
5 5
6 -Exhaustive approach for solving difficult cases of small open reading frame annotation: the PreImplantation Factor case 6 +Exhaustive approach for solving difficult cases of small open reading frame annotation: the PreImplantation Factor example
7 7
8 8
9 -The PreImplantation Factor: a difficult cases of small open reading frame annotation solved by an exhaustive approach 9 +The PreImplantation Factor: a difficult case of small open reading frame annotation solved by an exhaustive approach
10 10
11 11
12 12
......
1 +
2 +
3 +mutli-FASTA
4 +
5 +display name of alternate genetic code
6 +
7 +
8 +
9 +
1 +void select_genetic_code(string selection){
2 + cout << "Genetic code selected: " << selection << endl;
3 + // The Vertebrate Mitochondrial Code
4 + if (selection == "2"){
5 + gc_std["AGA"] = "*"; gc_std_DNA["AGA"] = "*"; gc_std_rev["UCU"] = "*"; gc_std_DNA_rev["TCT"] = "*";
6 + gc_std["AGG"] = "*"; gc_std_DNA["AGG"] = "*"; gc_std_rev["UCC"] = "*"; gc_std_DNA_rev["TCC"] = "*";
7 + gc_std["AGR"] = "*"; gc_std_DNA["AGR"] = "*"; gc_std_rev["UCY"] = "*"; gc_std_DNA_rev["TCY"] = "*";
8 + gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
9 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
10 + }
11 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
12 + else if (selection == "3"){
13 + gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
14 + gc_std["CUU"] = "T"; gc_std_DNA["CTT"] = "T"; gc_std_rev["GAA"] = "T"; gc_std_DNA_rev["GAA"] = "T";
15 + gc_std["CUC"] = "T"; gc_std_DNA["CTC"] = "T"; gc_std_rev["GAG"] = "T"; gc_std_DNA_rev["GAG"] = "T";
16 + gc_std["CUA"] = "T"; gc_std_DNA["CTA"] = "T"; gc_std_rev["GAU"] = "T"; gc_std_DNA_rev["GAT"] = "T";
17 + gc_std["CUG"] = "T"; gc_std_DNA["CTG"] = "T"; gc_std_rev["GAC"] = "T"; gc_std_DNA_rev["GAC"] = "T";
18 + gc_std["CUN"] = "T"; gc_std_DNA["CTN"] = "T"; gc_std_rev["GAN"] = "T"; gc_std_DNA_rev["GAN"] = "T";
19 + gc_std["CUR"] = "T"; gc_std_DNA["CTR"] = "T"; gc_std_rev["GAR"] = "T"; gc_std_DNA_rev["GAR"] = "T";
20 + gc_std["CUY"] = "T"; gc_std_DNA["CTY"] = "T"; gc_std_rev["GAY"] = "T"; gc_std_DNA_rev["GAY"] = "T";
21 + gc_std["CUM"] = "T"; gc_std_DNA["CTM"] = "T"; gc_std_rev["GAM"] = "T"; gc_std_DNA_rev["GAM"] = "T";
22 + gc_std["CUK"] = "T"; gc_std_DNA["CTK"] = "T"; gc_std_rev["GAK"] = "T"; gc_std_DNA_rev["GAK"] = "T";
23 + gc_std["CUS"] = "T"; gc_std_DNA["CTS"] = "T"; gc_std_rev["GAS"] = "T"; gc_std_DNA_rev["GAS"] = "T";
24 + gc_std["CUW"] = "T"; gc_std_DNA["CTW"] = "T"; gc_std_rev["GAW"] = "T"; gc_std_DNA_rev["GAW"] = "T";
25 + gc_std["CUH"] = "T"; gc_std_DNA["CTH"] = "T"; gc_std_rev["GAH"] = "T"; gc_std_DNA_rev["GAH"] = "T";
26 + gc_std["CUB"] = "T"; gc_std_DNA["CTB"] = "T"; gc_std_rev["GAB"] = "T"; gc_std_DNA_rev["GAB"] = "T";
27 + gc_std["CUV"] = "T"; gc_std_DNA["CTV"] = "T"; gc_std_rev["GAV"] = "T"; gc_std_DNA_rev["GAV"] = "T";
28 + gc_std["CUD"] = "T"; gc_std_DNA["CTD"] = "T"; gc_std_rev["GAD"] = "T"; gc_std_DNA_rev["GAD"] = "T";
29 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
30 + }
31 + // xxxxxxxxxxxxxxxxxxxxxxxx
32 + else if (selection == "4"){ // Mycoplasma
33 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
34 + }
35 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
36 + else if (selection == "5"){
37 + gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
38 + gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
39 + gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
40 + gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
41 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
42 + }
43 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
44 + else if (selection == "6"){
45 + gc_std["UAA"] = "Q"; gc_std_DNA["TAA"] = "Q"; gc_std_rev["AUU"] = "Q"; gc_std_DNA_rev["ATT"] = "Q";
46 + gc_std["UAG"] = "Q"; gc_std_DNA["TAG"] = "Q"; gc_std_rev["AUC"] = "Q"; gc_std_DNA_rev["ATC"] = "Q";
47 + gc_std["UAR"] = "Q"; gc_std_DNA["TAR"] = "Q"; gc_std_rev["AUY"] = "Q"; gc_std_DNA_rev["ATY"] = "Q";
48 + }
49 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
50 + else if (selection == "9"){
51 + gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
52 + gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
53 + gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
54 + gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
55 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
56 + }
57 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
58 + else if (selection == "10"){
59 + gc_std["UGA"] = "C"; gc_std_DNA["TGA"] = "C"; gc_std_rev["ACU"] = "C"; gc_std_DNA_rev["ACT"] = "C";
60 + }
61 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
62 + else if (selection == "12"){
63 + gc_std["CUG"] = "S"; gc_std_DNA["CTG"] = "S"; gc_std_rev["GAC"] = "S"; gc_std_DNA_rev["GAC"] = "S";
64 + }
65 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
66 + else if (selection == "13"){
67 + gc_std["AGA"] = "G"; gc_std_DNA["AGA"] = "G"; gc_std_rev["UCU"] = "G"; gc_std_DNA_rev["TCT"] = "G";
68 + gc_std["AGG"] = "G"; gc_std_DNA["AGG"] = "G"; gc_std_rev["UCC"] = "G"; gc_std_DNA_rev["TCC"] = "G";
69 + gc_std["AGR"] = "G"; gc_std_DNA["AGR"] = "G"; gc_std_rev["UCY"] = "G"; gc_std_DNA_rev["TCY"] = "G";
70 + gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
71 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
72 + }
73 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
74 + else if (selection == "14"){
75 + gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
76 + gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
77 + gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
78 + gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
79 + gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
80 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
81 + }
82 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
83 + else if (selection == "16"){
84 + gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
85 + }
86 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
87 + else if (selection == "21"){
88 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
89 + gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
90 + gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
91 + gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
92 + gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
93 + gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
94 + }
95 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
96 + else if (selection == "22"){
97 + gc_std["UCA"] = "*"; gc_std_DNA["TCA"] = "*"; gc_std_rev["AGU"] = "*"; gc_std_DNA_rev["AGT"] = "*";
98 + gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
99 + }
100 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
101 + else if (selection == "23"){
102 + gc_std["UUA"] = "*"; gc_std_DNA["TTA"] = "*"; gc_std_rev["AAU"] = "*"; gc_std_DNA_rev["AAT"] = "*";
103 + }
104 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
105 + else if (selection == "24"){
106 + gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
107 + gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
108 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
109 + }
110 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
111 + else if (selection == "25"){
112 + gc_std["UGA"] = "G"; gc_std_DNA["TGA"] = "G"; gc_std_rev["ACU"] = "G"; gc_std_DNA_rev["ACT"] = "G";
113 + }
114 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
115 + else if (selection == "26"){
116 + gc_std["CUG"] = "A"; gc_std_DNA["CTG"] = "A"; gc_std_rev["GAC"] = "A"; gc_std_DNA_rev["GAC"] = "A";
117 + }
118 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
119 + else if (selection == "29"){
120 + gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
121 + gc_std["UAG"] = "Y"; gc_std_DNA["TAG"] = "Y"; gc_std_rev["AUC"] = "Y"; gc_std_DNA_rev["ATC"] = "Y";
122 + gc_std["UAR"] = "Y"; gc_std_DNA["TAR"] = "Y"; gc_std_rev["AUY"] = "Y"; gc_std_DNA_rev["ATY"] = "Y";
123 + }
124 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
125 + else if (selection == "30"){
126 + gc_std["UAA"] = "E"; gc_std_DNA["TAA"] = "E"; gc_std_rev["AUU"] = "E"; gc_std_DNA_rev["ATT"] = "E";
127 + gc_std["UAG"] = "E"; gc_std_DNA["TAG"] = "E"; gc_std_rev["AUC"] = "E"; gc_std_DNA_rev["ATC"] = "E";
128 + gc_std["UAR"] = "E"; gc_std_DNA["TAR"] = "E"; gc_std_rev["AUY"] = "E"; gc_std_DNA_rev["ATY"] = "E";
129 + }
130 + // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
131 + else if (selection == "33"){
132 + gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
133 + gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
134 + gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
135 + gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
136 + }
137 +}
138 +
139 +// -11, (-27, -28, -31)
140 +
141 +
142 + // N R Y M K S W H B V D
143 + // N Y R K M S W D V B H
144 +
145 +
...@@ -7,6 +7,7 @@ ...@@ -7,6 +7,7 @@
7 #include <algorithm> 7 #include <algorithm>
8 #include <vector> 8 #include <vector>
9 #include "split.h" 9 #include "split.h"
10 +#include "alternate_codes.h"
10 11
11 // system detection 12 // system detection
12 // docker 13 // docker
...@@ -15,12 +16,35 @@ ...@@ -15,12 +16,35 @@
15 /* Global variables */ 16 /* Global variables */
16 vector<int> multiFASTA_seqlen; 17 vector<int> multiFASTA_seqlen;
17 map<string, string> genetic_code; 18 map<string, string> genetic_code;
18 -vector<string> sCodon; 19 +vector<string> sCodons;
19 int minimum_length = 0; 20 int minimum_length = 0;
20 21
21 22
22 // XXX PROTOTYPES 23 // XXX PROTOTYPES
23 24
25 +vector<string> complement_sCodons(vector<string> vec_codons, bool rna){
26 + vector<string> cvec_codons;
27 + for (string sCodon : vec_codons){
28 + string codonCompl;
29 + for (char& c : sCodon){
30 + if (c == 'A'){
31 + (rna) ? codonCompl+='U' : codonCompl+='T';
32 + }
33 + if (c == 'C'){
34 + codonCompl+='G';
35 + }
36 + if (c == 'G'){
37 + codonCompl+='C';
38 + }
39 + if (c == 'T'){
40 + codonCompl+='A';
41 + }
42 + }
43 + cvec_codons.push_back(codonCompl);
44 + }
45 + return cvec_codons;
46 +}
47 +
24 48
25 void extend_until_print(string &codon, string &protein, string &nucleic, int frame, char posneg, ofstream &outfile, ofstream &outfileDNA, bool backward, int position, int glob_vec_index){ 49 void extend_until_print(string &codon, string &protein, string &nucleic, int frame, char posneg, ofstream &outfile, ofstream &outfileDNA, bool backward, int position, int glob_vec_index){
26 if (codon.length() == 3){ 50 if (codon.length() == 3){
...@@ -42,8 +66,8 @@ void extend_until_print(string &codon, string &protein, string &nucleic, int fra ...@@ -42,8 +66,8 @@ void extend_until_print(string &codon, string &protein, string &nucleic, int fra
42 66
43 //reverse( nucleic.begin(), nucleic.end() ); // XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX 67 //reverse( nucleic.begin(), nucleic.end() ); // XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX
44 68
45 - if (!sCodon.empty()){ 69 + if (!sCodons.empty()){
46 - if (find(sCodon.begin(), sCodon.end(), nucleic.substr(0, 3)) != sCodon.end()){ // if nucleic codon is in the vector of start codons 70 + if (find(sCodons.begin(), sCodons.end(), nucleic.substr(0, 3)) != sCodons.end()){ // if nucleic codon is in the vector of start codons
47 outfile << frame << posneg << "\t" << begin << "-" << position << "\t" << protein << "\n"; 71 outfile << frame << posneg << "\t" << begin << "-" << position << "\t" << protein << "\n";
48 outfileDNA << frame << posneg << "\t" << begin << "-" << position << "\t" << nucleic << "\n"; 72 outfileDNA << frame << posneg << "\t" << begin << "-" << position << "\t" << nucleic << "\n";
49 } 73 }
...@@ -169,126 +193,6 @@ int check_file_content(string fastaFileName, bool rna){ ...@@ -169,126 +193,6 @@ int check_file_content(string fastaFileName, bool rna){
169 } 193 }
170 194
171 195
172 -void select_genetic_code(string selection){
173 - cout << "Genetic code selected: " << selection << endl;
174 - // The Vertebrate Mitochondrial Code
175 - if (selection == "2"){
176 - gc_std["AGA"] = "*"; gc_std_DNA["AGA"] = "*"; gc_std_rev["UCU"] = "*"; gc_std_DNA_rev["TCT"] = "*";
177 - gc_std["AGG"] = "*"; gc_std_DNA["AGG"] = "*"; gc_std_rev["UCC"] = "*"; gc_std_DNA_rev["TCC"] = "*";
178 - gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
179 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
180 - }
181 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
182 - else if (selection == "3"){
183 - gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
184 - gc_std["CUU"] = "T"; gc_std_DNA["CTT"] = "T"; gc_std_rev["GAA"] = "T"; gc_std_DNA_rev["GAA"] = "T";
185 - gc_std["CUC"] = "T"; gc_std_DNA["CTC"] = "T"; gc_std_rev["GAG"] = "T"; gc_std_DNA_rev["GAG"] = "T";
186 - gc_std["CUA"] = "T"; gc_std_DNA["CTA"] = "T"; gc_std_rev["GAU"] = "T"; gc_std_DNA_rev["GAT"] = "T";
187 - gc_std["CUG"] = "T"; gc_std_DNA["CTG"] = "T"; gc_std_rev["GAC"] = "T"; gc_std_DNA_rev["GAC"] = "T";
188 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
189 - }
190 - // xxxxxxxxxxxxxxxxxxxxxxxx
191 - else if (selection == "4"){ // Mycoplasma
192 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
193 - }
194 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
195 - else if (selection == "5"){
196 - gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
197 - gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
198 - gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
199 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
200 - }
201 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
202 - else if (selection == "6"){
203 - gc_std["UAA"] = "Q"; gc_std_DNA["TAA"] = "Q"; gc_std_rev["AUU"] = "Q"; gc_std_DNA_rev["ATT"] = "Q";
204 - gc_std["UAG"] = "Q"; gc_std_DNA["TAG"] = "Q"; gc_std_rev["AUC"] = "Q"; gc_std_DNA_rev["ATC"] = "Q";
205 - }
206 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
207 - else if (selection == "9"){
208 - gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
209 - gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
210 - gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
211 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
212 - }
213 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
214 - else if (selection == "10"){
215 - gc_std["UGA"] = "C"; gc_std_DNA["TGA"] = "C"; gc_std_rev["ACU"] = "C"; gc_std_DNA_rev["ACT"] = "C";
216 - }
217 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
218 - else if (selection == "12"){
219 - gc_std["CUG"] = "S"; gc_std_DNA["CTG"] = "S"; gc_std_rev["GAC"] = "S"; gc_std_DNA_rev["GAC"] = "S";
220 - }
221 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
222 - else if (selection == "13"){
223 - gc_std["AGA"] = "G"; gc_std_DNA["AGA"] = "G"; gc_std_rev["UCU"] = "G"; gc_std_DNA_rev["TCT"] = "G";
224 - gc_std["AGG"] = "G"; gc_std_DNA["AGG"] = "G"; gc_std_rev["UCC"] = "G"; gc_std_DNA_rev["TCC"] = "G";
225 - gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
226 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
227 - }
228 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
229 - else if (selection == "14"){
230 - gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
231 - gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
232 - gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
233 - gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
234 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
235 - }
236 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
237 - else if (selection == "16"){
238 - gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
239 - }
240 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
241 - else if (selection == "21"){
242 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
243 - gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
244 - gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
245 - gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
246 - gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
247 - }
248 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
249 - else if (selection == "22"){
250 - gc_std["UCA"] = "*"; gc_std_DNA["TCA"] = "*"; gc_std_rev["AGU"] = "*"; gc_std_DNA_rev["AGT"] = "*";
251 - gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
252 - }
253 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
254 - else if (selection == "23"){
255 - gc_std["UUA"] = "*"; gc_std_DNA["TTA"] = "*"; gc_std_rev["AAU"] = "*"; gc_std_DNA_rev["AAT"] = "*";
256 - }
257 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
258 - else if (selection == "24"){
259 - gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
260 - gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
261 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
262 - }
263 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
264 - else if (selection == "25"){
265 - gc_std["UGA"] = "G"; gc_std_DNA["TGA"] = "G"; gc_std_rev["ACU"] = "G"; gc_std_DNA_rev["ACT"] = "G";
266 - }
267 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
268 - else if (selection == "26"){
269 - gc_std["CUG"] = "A"; gc_std_DNA["CTG"] = "A"; gc_std_rev["GAC"] = "A"; gc_std_DNA_rev["GAC"] = "A";
270 - }
271 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
272 - else if (selection == "29"){
273 - gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
274 - gc_std["UAG"] = "Y"; gc_std_DNA["TAG"] = "Y"; gc_std_rev["AUC"] = "Y"; gc_std_DNA_rev["ATC"] = "Y";
275 - }
276 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
277 - else if (selection == "30"){
278 - gc_std["UAA"] = "E"; gc_std_DNA["TAA"] = "E"; gc_std_rev["AUU"] = "E"; gc_std_DNA_rev["ATT"] = "E";
279 - gc_std["UAG"] = "E"; gc_std_DNA["TAG"] = "E"; gc_std_rev["AUC"] = "E"; gc_std_DNA_rev["ATC"] = "E";
280 - }
281 - // xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
282 - else if (selection == "33"){
283 - gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
284 - gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
285 - gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
286 - gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
287 - }
288 -}
289 -
290 -// -11, (-27, -28, -31)
291 -
292 // input list of files XXX 196 // input list of files XXX
293 197
294 198
...@@ -344,7 +248,8 @@ int main(int argc, char** argv){ ...@@ -344,7 +248,8 @@ int main(int argc, char** argv){
344 puts("Start codon: no specific amino acid selected"); 248 puts("Start codon: no specific amino acid selected");
345 } 249 }
346 else{ 250 else{
347 - sCodon = split(startCodon, '-'); 251 + sCodons = split(startCodon, '-');
252 + // XXX Check alternate
348 } 253 }
349 254
350 /* Check input file content */ 255 /* Check input file content */
...@@ -361,8 +266,7 @@ int main(int argc, char** argv){ ...@@ -361,8 +266,7 @@ int main(int argc, char** argv){
361 266
362 /* Modifications to the standard genetic code */ 267 /* Modifications to the standard genetic code */
363 select_genetic_code(alt_gene_code); 268 select_genetic_code(alt_gene_code);
364 - // XXX option pour Alternative Initiation Codons 269 + // XXX Check value
365 - // OU BIEN fichier txt lu
366 270
367 271
368 /* Filenames: temporary AND final output */ 272 /* Filenames: temporary AND final output */
...@@ -406,6 +310,7 @@ int main(int argc, char** argv){ ...@@ -406,6 +310,7 @@ int main(int argc, char** argv){
406 /* Translation 3'-5' */ 310 /* Translation 3'-5' */
407 puts("3'-5' translation..."); 311 puts("3'-5' translation...");
408 (rna) ? genetic_code = gc_std_rev : genetic_code = gc_std_DNA_rev; 312 (rna) ? genetic_code = gc_std_rev : genetic_code = gc_std_DNA_rev;
313 + sCodons = complement_sCodons(sCodons, rna);
409 translate_3_frames(tmp_reversed_input, tmp_35_pro_file, tmp_35_dna_file, true); 314 translate_3_frames(tmp_reversed_input, tmp_35_pro_file, tmp_35_dna_file, true);
410 puts("Done"); 315 puts("Done");
411 316
......