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932 additions
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218 deletions
... | @@ -44,6 +44,7 @@ namespace import { | ... | @@ -44,6 +44,7 @@ namespace import { |
44 | */ | 44 | */ |
45 | class Fasta : public multithread::Buffer_producer<data::Data_basic*>{ | 45 | class Fasta : public multithread::Buffer_producer<data::Data_basic*>{ |
46 | std::string file; | 46 | std::string file; |
47 | + unsigned int length_min; | ||
47 | protected: | 48 | protected: |
48 | void work_out(){ | 49 | void work_out(){ |
49 | std::cout << "Start fasta reader : " << this->file << std::endl; | 50 | std::cout << "Start fasta reader : " << this->file << std::endl; |
... | @@ -59,7 +60,7 @@ namespace import { | ... | @@ -59,7 +60,7 @@ namespace import { |
59 | int idx(1); | 60 | int idx(1); |
60 | while(std::getline(input,line).good()){ | 61 | while(std::getline(input,line).good()){ |
61 | if(line.empty() || line[0] == '>'){ | 62 | if(line.empty() || line[0] == '>'){ |
62 | - if(!id.empty()){ | 63 | + if(!id.empty() && sequence.size() > this->length_min){ |
63 | this->push(new entry::Sequence(id,sequence)); | 64 | this->push(new entry::Sequence(id,sequence)); |
64 | idx ++; | 65 | idx ++; |
65 | } | 66 | } |
... | @@ -80,7 +81,7 @@ namespace import { | ... | @@ -80,7 +81,7 @@ namespace import { |
80 | } | 81 | } |
81 | } | 82 | } |
82 | } | 83 | } |
83 | - if( !id.empty() ){ | 84 | + if(!id.empty() && sequence.size() > this->length_min){ |
84 | this->push(new entry::Sequence(id,sequence)); | 85 | this->push(new entry::Sequence(id,sequence)); |
85 | } | 86 | } |
86 | std::cout << "End fasta reader" << std::endl; | 87 | std::cout << "End fasta reader" << std::endl; |
... | @@ -94,7 +95,7 @@ namespace import { | ... | @@ -94,7 +95,7 @@ namespace import { |
94 | * @param buffer_size a int, the size of the internal buffer | 95 | * @param buffer_size a int, the size of the internal buffer |
95 | */ | 96 | */ |
96 | Fasta(multithread::Buffer<data::Data_basic*> *out,std::string file): | 97 | Fasta(multithread::Buffer<data::Data_basic*> *out,std::string file): |
97 | - multithread::Buffer_producer<data::Data_basic*>(out),file(file){} | 98 | + multithread::Buffer_producer<data::Data_basic*>(out),file(file),length_min(5){} |
98 | }; | 99 | }; |
99 | } | 100 | } |
100 | 101 | ... | ... |
... | @@ -4,8 +4,7 @@ | ... | @@ -4,8 +4,7 @@ |
4 | #include <chrono> | 4 | #include <chrono> |
5 | 5 | ||
6 | const int THREAD_NB = 4; | 6 | const int THREAD_NB = 4; |
7 | -const std::chrono::milliseconds THREAD_SLEEP(2); | 7 | +const std::chrono::milliseconds THREAD_SLEEP(1); |
8 | -const int BUFFER_SIZE = 500; | 8 | +const int BUFFER_SIZE = 100; |
9 | -const int NB_ELT_BUF = 100; | ||
10 | 9 | ||
11 | #endif // CONSTANT_H | 10 | #endif // CONSTANT_H | ... | ... |
... | @@ -7,6 +7,7 @@ | ... | @@ -7,6 +7,7 @@ |
7 | 7 | ||
8 | #include "feature.h" | 8 | #include "feature.h" |
9 | #include "feature_callable.h" | 9 | #include "feature_callable.h" |
10 | +#include "util.h" | ||
10 | 11 | ||
11 | namespace feature { | 12 | namespace feature { |
12 | const std::vector<std::string> ORF::START{"AUG","ATG","TTG","UUG","CTG","CUG"}; | 13 | const std::vector<std::string> ORF::START{"AUG","ATG","TTG","UUG","CTG","CUG"}; |
... | @@ -125,7 +126,17 @@ std::string ORF::to_dict(){ | ... | @@ -125,7 +126,17 @@ std::string ORF::to_dict(){ |
125 | } | 126 | } |
126 | 127 | ||
127 | std::string ORF::to_csv(){ | 128 | std::string ORF::to_csv(){ |
128 | - return this->name+","+std::to_string(this->length) + ","+ std::to_string(this->coverage) + "," + std::to_string(this->start_mean) + "," + std::to_string(this->start_std) + "," + std::to_string(this->end_mean) + "," + std::to_string(this->end_std); | 129 | + return this->name+"," + |
130 | + std::to_string(this->length) + "," + | ||
131 | + std::to_string(this->coverage) + "," + | ||
132 | + std::to_string(this->coverage_all_mean) + "," + | ||
133 | + std::to_string(this->coverage_all_std) + "," + | ||
134 | + std::to_string(this->frame_biases) + "," + | ||
135 | + std::to_string(this->frequency) + "," + | ||
136 | + std::to_string(this->start_mean) + "," + | ||
137 | + std::to_string(this->start_std) + "," + | ||
138 | + std::to_string(this->end_mean) + "," + | ||
139 | + std::to_string(this->end_std); | ||
129 | } | 140 | } |
130 | 141 | ||
131 | std::string CodonBiases::to_dict(){ | 142 | std::string CodonBiases::to_dict(){ |
... | @@ -149,7 +160,8 @@ std::string CodonBiases::to_csv(){ | ... | @@ -149,7 +160,8 @@ std::string CodonBiases::to_csv(){ |
149 | std::to_string(this->composition[0]) + ","+ | 160 | std::to_string(this->composition[0]) + ","+ |
150 | std::to_string(this->composition[1]) + ","+ | 161 | std::to_string(this->composition[1]) + ","+ |
151 | std::to_string(this->composition[2]) + ","+ | 162 | std::to_string(this->composition[2]) + ","+ |
152 | - std::to_string(this->composition[3]); | 163 | + std::to_string(this->composition[3])+ ","+ |
164 | + std::to_string(this->gc_content); | ||
153 | } | 165 | } |
154 | 166 | ||
155 | // Constructor | 167 | // Constructor |
... | @@ -157,7 +169,7 @@ std::string CodonBiases::to_csv(){ | ... | @@ -157,7 +169,7 @@ std::string CodonBiases::to_csv(){ |
157 | // Kmer | 169 | // Kmer |
158 | Kmer::Kmer(entry::Sequence &s, const unsigned int &k):Feature(s.getName()),k(k){ | 170 | Kmer::Kmer(entry::Sequence &s, const unsigned int &k):Feature(s.getName()),k(k){ |
159 | std::string seq = s.getSeq(); | 171 | std::string seq = s.getSeq(); |
160 | - for(unsigned int i(0); i < s.getLength() - this->k - 1; i++){ | 172 | + for(unsigned int i(0); i < s.getLength() - this->k + 1; i++){ |
161 | std::string kmer = seq.substr(i,this->k); | 173 | std::string kmer = seq.substr(i,this->k); |
162 | std::transform(kmer.begin(),kmer.end(),kmer.begin(),::toupper); | 174 | std::transform(kmer.begin(),kmer.end(),kmer.begin(),::toupper); |
163 | std::replace(kmer.begin(),kmer.end(),'U','T'); | 175 | std::replace(kmer.begin(),kmer.end(),'U','T'); |
... | @@ -180,7 +192,7 @@ ORF::ORF(const entry::Sequence &s):Feature(s.getName()),length(0){ | ... | @@ -180,7 +192,7 @@ ORF::ORF(const entry::Sequence &s):Feature(s.getName()),length(0){ |
180 | std::transform(seq.begin(),seq.end(),seq.begin(),toupper); | 192 | std::transform(seq.begin(),seq.end(),seq.begin(),toupper); |
181 | std::vector<unsigned int> start_codon; | 193 | std::vector<unsigned int> start_codon; |
182 | std::vector<unsigned int> end_codon; | 194 | std::vector<unsigned int> end_codon; |
183 | - std::pair<unsigned int, unsigned int> orf_pair; | 195 | + std::vector<std::tuple<unsigned int, unsigned int, unsigned int, unsigned int>> orfs; |
184 | //find position codon start and stop | 196 | //find position codon start and stop |
185 | for(unsigned int i(0); i < seq.length(); i++){ | 197 | for(unsigned int i(0); i < seq.length(); i++){ |
186 | std::string tmp = seq.substr(i,3); | 198 | std::string tmp = seq.substr(i,3); |
... | @@ -200,9 +212,10 @@ ORF::ORF(const entry::Sequence &s):Feature(s.getName()),length(0){ | ... | @@ -200,9 +212,10 @@ ORF::ORF(const entry::Sequence &s):Feature(s.getName()),length(0){ |
200 | for(auto const &end_pos: end_codon){ | 212 | for(auto const &end_pos: end_codon){ |
201 | if(start_pos < end_pos){ | 213 | if(start_pos < end_pos){ |
202 | unsigned int length = end_pos - start_pos; | 214 | unsigned int length = end_pos - start_pos; |
215 | + unsigned int frame = start_pos % 3; | ||
203 | if((length%3 == 0)){ | 216 | if((length%3 == 0)){ |
217 | + orfs.push_back(std::tuple<unsigned int, unsigned int, unsigned int, unsigned int>(frame,length,start_pos,end_pos)); | ||
204 | if(length > this->length){ | 218 | if(length > this->length){ |
205 | - orf_pair = std::pair<unsigned int, unsigned int>(start_pos,end_pos); | ||
206 | this->length = length; | 219 | this->length = length; |
207 | } | 220 | } |
208 | break; | 221 | break; |
... | @@ -211,33 +224,38 @@ ORF::ORF(const entry::Sequence &s):Feature(s.getName()),length(0){ | ... | @@ -211,33 +224,38 @@ ORF::ORF(const entry::Sequence &s):Feature(s.getName()),length(0){ |
211 | } | 224 | } |
212 | } | 225 | } |
213 | } | 226 | } |
214 | - this->coverage = static_cast<float>(this->length) / s.getLength(); | ||
215 | - this->length = log10(this->length); | ||
216 | - this->start_mean = 0; | ||
217 | - for(auto const &start_pos: start_codon){ | ||
218 | - this->start_mean += start_pos; | ||
219 | - } | ||
220 | - this->start_mean /= start_codon.size(); | ||
221 | - | ||
222 | - this->start_std = 0; | ||
223 | - for(auto const &start_pos: start_codon){ | ||
224 | - this->start_std += pow(start_pos - this->start_mean,2.0); | ||
225 | - } | ||
226 | - this->start_std = sqrt(this->start_mean)/start_codon.size() / s.getLength(); | ||
227 | - this->start_mean /= s.getLength(); | ||
228 | 227 | ||
229 | - this->end_mean = 0; | 228 | + if(orfs.size() > 0){ |
230 | - for(auto const &end_pos: end_codon){ | 229 | + int orf_per_frame[3] = {0,0,0}; |
231 | - this->end_mean += end_pos; | 230 | + for(auto const &orf: orfs){ |
232 | - } | 231 | + this->coverage_all_mean += static_cast<float>(std::get<1>(orf))/s.getLength(); |
233 | - this->end_mean /= end_codon.size(); | 232 | + orf_per_frame[std::get<0>(orf)] += 1; |
233 | + this->start_mean += std::get<2>(orf); | ||
234 | + this->end_mean += std::get<3>(orf); | ||
235 | + } | ||
236 | + this->start_mean = this->start_mean / orfs.size() / s.getLength(); | ||
237 | + this->end_mean = this->end_mean / orfs.size() /s.getLength(); | ||
238 | + this->coverage_all_mean = this->coverage_all_mean / orfs.size(); | ||
239 | + this->frequency = static_cast<float>(orfs.size())/start_codon.size(); | ||
240 | + | ||
241 | + auto mm = std::minmax_element(std::begin(orf_per_frame),std::end(orf_per_frame)); | ||
242 | + this->frame_biases = 1.0 - static_cast<float>(*mm.first)/ | ||
243 | + static_cast<float>(*mm.second); | ||
244 | + | ||
245 | + for(auto const &orf: orfs){ | ||
246 | + this->coverage_all_std += pow(static_cast<float>(std::get<1>(orf))/s.getLength() - this->coverage_all_mean,2.0); | ||
247 | + this->start_std += pow(static_cast<float>(std::get<2>(orf))/s.getLength() - this->start_mean,2.0); | ||
248 | + this->end_std += pow(static_cast<float>(std::get<3>(orf))/s.getLength() - this->end_mean,2.0); | ||
249 | + } | ||
250 | + this->coverage_all_std =sqrt(this->coverage_all_std / orfs.size()); | ||
251 | + this->start_std = sqrt(this->start_std / orfs.size()); | ||
252 | + this->end_std = sqrt(this->end_std / orfs.size()); | ||
253 | + | ||
234 | 254 | ||
235 | - this->end_std = 0; | 255 | + this->coverage = static_cast<float>(this->length) / s.getLength(); |
236 | - for(auto const &end_pos: end_codon){ | 256 | + //this->length = exp(-static_cast<float>(this->length)/200.0); |
237 | - this->end_std += pow(end_pos - this->end_mean,2.0); | 257 | + this->length = log10(static_cast<float>(this->length)); |
238 | } | 258 | } |
239 | - this->end_std = sqrt(this->end_mean)/end_codon.size() / s.getLength(); | ||
240 | - this->end_mean /= s.getLength(); | ||
241 | } | 259 | } |
242 | 260 | ||
243 | // Codon position | 261 | // Codon position |
... | @@ -257,6 +275,7 @@ CodonBiases::CodonBiases(const entry::Sequence &seq):Feature(seq.getName()){ | ... | @@ -257,6 +275,7 @@ CodonBiases::CodonBiases(const entry::Sequence &seq):Feature(seq.getName()){ |
257 | case 'c': | 275 | case 'c': |
258 | mat[3+(i%3)] += 1; | 276 | mat[3+(i%3)] += 1; |
259 | this->composition[1] += 1; | 277 | this->composition[1] += 1; |
278 | + this->gc_content += 1; | ||
260 | break; | 279 | break; |
261 | case 'T': | 280 | case 'T': |
262 | case 't': | 281 | case 't': |
... | @@ -269,16 +288,18 @@ CodonBiases::CodonBiases(const entry::Sequence &seq):Feature(seq.getName()){ | ... | @@ -269,16 +288,18 @@ CodonBiases::CodonBiases(const entry::Sequence &seq):Feature(seq.getName()){ |
269 | case 'g': | 288 | case 'g': |
270 | mat[9+(i%3)] += 1; | 289 | mat[9+(i%3)] += 1; |
271 | this->composition[3] += 1; | 290 | this->composition[3] += 1; |
291 | + this->gc_content += 1; | ||
272 | break; | 292 | break; |
273 | } | 293 | } |
274 | } | 294 | } |
275 | for(int i(0); i < 4; i++){ | 295 | for(int i(0); i < 4; i++){ |
276 | std::valarray<int> tmp(mat[std::slice(i*3,3,1)]); | 296 | std::valarray<int> tmp(mat[std::slice(i*3,3,1)]); |
277 | - auto mm = std::minmax_element(begin(tmp),end(tmp)); | 297 | + auto mm = std::minmax_element(std::begin(tmp),std::end(tmp)); |
278 | this->position[i] = static_cast<float>(*mm.first)/ | 298 | this->position[i] = static_cast<float>(*mm.first)/ |
279 | (static_cast<float>(*mm.second) + 1.0); | 299 | (static_cast<float>(*mm.second) + 1.0); |
280 | this->composition[i] /= seq.getLength(); | 300 | this->composition[i] /= seq.getLength(); |
281 | } | 301 | } |
302 | + this->gc_content /= seq.getLength(); | ||
282 | } | 303 | } |
283 | 304 | ||
284 | // Dist | 305 | // Dist | ... | ... |
... | @@ -98,12 +98,17 @@ protected: | ... | @@ -98,12 +98,17 @@ protected: |
98 | static const std::vector<std::string> END; | 98 | static const std::vector<std::string> END; |
99 | static bool in_start(const std::string &c); | 99 | static bool in_start(const std::string &c); |
100 | static bool in_end(const std::string &c); | 100 | static bool in_end(const std::string &c); |
101 | - unsigned int length; | 101 | + float length=0; |
102 | - float coverage; | 102 | + float coverage=0; |
103 | - float start_mean; | 103 | + float coverage_all_mean=0; |
104 | - float start_std; | 104 | + float coverage_all_std=0; |
105 | - float end_mean; | 105 | + float frame_biases=0; |
106 | - float end_std; | 106 | + float frequency=0; |
107 | + | ||
108 | + float start_mean=0; | ||
109 | + float start_std=0; | ||
110 | + float end_mean=0; | ||
111 | + float end_std=0; | ||
107 | 112 | ||
108 | /* | 113 | /* |
109 | float start_center, start_std; | 114 | float start_center, start_std; |
... | @@ -144,6 +149,7 @@ public: | ... | @@ -144,6 +149,7 @@ public: |
144 | class CodonBiases: public feature::Feature{ | 149 | class CodonBiases: public feature::Feature{ |
145 | protected: | 150 | protected: |
146 | float position[4] = {0,0,0,0}; | 151 | float position[4] = {0,0,0,0}; |
152 | + float gc_content = 0; | ||
147 | float composition[4] = {0,0,0,0}; | 153 | float composition[4] = {0,0,0,0}; |
148 | void init(const Data_basic *db); | 154 | void init(const Data_basic *db); |
149 | public: | 155 | public: | ... | ... |
... | @@ -55,7 +55,17 @@ int main(int argc, char* argv[]) | ... | @@ -55,7 +55,17 @@ int main(int argc, char* argv[]) |
55 | feature::Feature_callable *kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(3)); | 55 | feature::Feature_callable *kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(3)); |
56 | tmp_ds = new data::Data_Store_Map(output+"KMER3.txt"); | 56 | tmp_ds = new data::Data_Store_Map(output+"KMER3.txt"); |
57 | ds["KMER3"] = tmp_ds; | 57 | ds["KMER3"] = tmp_ds; |
58 | - create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re); | 58 | + create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(3),tmp_ds,&re); |
59 | + | ||
60 | + kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(4)); | ||
61 | + tmp_ds = new data::Data_Store_Map(output+"KMER4.txt"); | ||
62 | + ds["KMER4"] = tmp_ds; | ||
63 | + create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(4),tmp_ds,&re); | ||
64 | + | ||
65 | + kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(5)); | ||
66 | + tmp_ds = new data::Data_Store_Map(output+"KMER5.txt"); | ||
67 | + ds["KMER5"] = tmp_ds; | ||
68 | + create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(5),tmp_ds,&re); | ||
59 | 69 | ||
60 | // kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(6)); | 70 | // kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(6)); |
61 | // tmp_ds = new data::Data_Store_Map(output+"KMER6.txt"); | 71 | // tmp_ds = new data::Data_Store_Map(output+"KMER6.txt"); | ... | ... |
... | @@ -28,4 +28,15 @@ void tokenize(const std::string& str, ContainerT& tokens, | ... | @@ -28,4 +28,15 @@ void tokenize(const std::string& str, ContainerT& tokens, |
28 | } | 28 | } |
29 | } | 29 | } |
30 | 30 | ||
31 | +template <class T> | ||
32 | +std::pair<T,T> minmax(T tab[],unsigned int size){ | ||
33 | + T min = tab[0]; | ||
34 | + T max = tab[0]; | ||
35 | + for(unsigned int i=0; i < size; i++){ | ||
36 | + min = (min > tab[i]) ? tab[i] : min; | ||
37 | + max = (max < tab[i]) ? tab[i] : max; | ||
38 | + } | ||
39 | + return std::pair<T,T>(min,max); | ||
40 | +} | ||
41 | + | ||
31 | #endif // UTIL_H | 42 | #endif // UTIL_H | ... | ... |
No preview for this file type
1 | -1.984570588223544485e+00 -1.952737297703042829e+00 | 1 | +-7.823954466377507355e-01 1.758610312279721644e+00 |
2 | -1.774149608263766220e+00 -2.077425117764972740e+00 | 2 | +-5.312403122381126330e-01 4.184234436232182053e-01 |
3 | --1.796766294253583085e-01 -4.313306443543813914e-03 | 3 | +8.399327166604406703e-01 -7.000761187943018715e-01 |
4 | -1.428676610906795208e+00 -1.731478714424572685e+00 | 4 | +-1.939753060347286784e+00 -5.791090073473343924e-01 |
5 | -1.433729758866031379e+00 -1.420659661802653462e+00 | 5 | +-9.625247053542576037e-01 1.631037196907302089e+00 |
6 | -2.181104524756568297e-01 -1.468106835733535565e-01 | 6 | +-1.458039677258911704e+00 -4.890695672382004422e-01 |
7 | --1.738711435514443293e+00 1.493139282756335673e+00 | 7 | +1.121869058141873543e+00 4.975141466460748091e-02 |
8 | --1.784778007759598939e+00 1.839502577357342128e+00 | 8 | +-5.918849912178264505e-01 7.924218704878657205e-01 |
9 | --1.087720778747320871e+00 9.695425106035429064e-01 | 9 | +3.665191049019017600e-01 -3.656267920978125696e-01 |
10 | +7.263957366062160359e-01 -4.689241974619325348e-01 | ||
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19 | +-8.299877483928708166e-01 1.856213755539437571e+00 | ||
20 | +1.476953518783209240e+00 -1.132759455664710702e+00 | ||
21 | +-5.632476301547526543e-01 1.180227950828089956e+00 | ||
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23 | +-9.459833419736710658e-01 9.965849028804589782e-01 | ||
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27 | +-1.146025504051904287e+00 1.320862723716864362e-01 | ||
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31 | +-2.101108507302599238e-01 4.369382169680571248e-01 | ||
32 | +1.368803982408707709e+00 1.072813569505477321e-01 | ||
33 | +2.144028850151701304e-01 6.472327452403894288e-01 | ||
34 | +7.323932189006194804e-01 -5.328193177645460521e-01 | ||
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36 | +3.219891756785852044e-01 1.148431544461899101e+00 | ||
37 | +-1.701638675611786555e-01 -3.866467322158495534e-01 | ||
38 | +1.464629796042067778e+00 2.307405632527817219e-01 | ||
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This diff could not be displayed because it is too large.
model/Arabidopsis/perf.txt
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model/Arabidopsis/plot_Codon_Bias.png
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model/Arabidopsis/plot_ORF.png
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model/Arabidopsis/plot_density.png
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model/Arabidopsis/plot_repartition_pred.png
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model/Arabidopsis/plot_repartition_true.png
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model/Drosophila/perf.txt
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model/Drosophila/plot_Codon_Bias.png
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model/Drosophila/plot_ORF.png
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model/Drosophila/plot_density.png
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model/Drosophila/plot_repartition_pred.png
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model/Drosophila/plot_repartition_true.png
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This diff could not be displayed because it is too large.
model/Escherichia_coli/perf.txt
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model/Escherichia_coli/plot_Codon_Bias.png
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model/Escherichia_coli/plot_ORF.png
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model/Escherichia_coli/plot_density.png
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This diff could not be displayed because it is too large.
model/Human/perf.txt
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model/Human/plot_Codon_Bias.png
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model/Human/plot_ORF.png
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model/Human/plot_density.png
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model/Human/plot_repartition.png
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model/Human/plot_repartition_pred.png
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model/Human/plot_repartition_true.png
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This diff could not be displayed because it is too large.
model/Mouse/perf.txt
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model/Mouse/plot_Codon_Bias.png
0 → 100644
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model/Mouse/plot_ORF.png
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model/Mouse/plot_density.png
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model/Mouse/plot_repartition.png
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model/Mouse/plot_repartition_pred.png
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model/Mouse/plot_repartition_true.png
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model/Oryza/SLSOM/W.txt
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model/Oryza/SLSOM/biases.txt
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model/Oryza/SLSOM/parameters.txt
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1 | +nb_label 2 |
model/Oryza/SOM/parameters.txt
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model/Oryza/SOM/units.txt
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model/Oryza/plot_Codon_Bias.png
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model/Oryza/plot_ORF.png
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model/Oryza/plot_density.png
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model/Oryza/plot_repartition_pred.png
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model/Oryza/plot_repartition_true.png
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100 | +2.784696540815985721e-01 1.029396887843844421e+00 | ... | ... |
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model/Saccharomyces_cerevisae/plot_ORF.png
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100 | +-4.081089260610661906e-01 6.552616602234176968e-01 | ... | ... |
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model/Zebrafish/perf.txt
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model/Zebrafish/plot_Codon_Bias.png
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model/Zebrafish/plot_ORF.png
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model/Zebrafish/plot_repartition.png
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model/Zebrafish/plot_repartition_true.png
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model/all_species/SLSOM/biases.txt
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model/all_species/SOM/parameters.txt
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model/all_species/plot_Codon_Bias.png
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model/all_species/plot_ORF.png
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model/all_species/plot_density.png
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