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Commit 9a6ba918 authored by Yannis's avatar Yannis
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implementation of reference, genes and annotations reading

parent 3de107cf
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Showing with 216 additions and 211 deletions
cpp/utils.h 100644 → 100755
View file @ 9a6ba918
#ifndef _UTILS_H #ifndef _UTILS_H
#define _UTILS_H #define _UTILS_H
#include <vector>
bool IsFileReadable( std::string ); bool IsFileReadable( std::string );
void ExecMeasure( struct timeval, struct timeval, std::string ); void ExecMeasure( struct timeval, struct timeval, std::string );
...@@ -10,5 +12,8 @@ std::string int_to_string( int ); ...@@ -10,5 +12,8 @@ std::string int_to_string( int );
char checkBase(char); char checkBase(char);
std::string pyReplace( std::string , std::string , std::string ); std::string pyReplace( std::string , std::string , std::string );
std::string char_to_string(char); std::string char_to_string(char);
std::vector<std::string> parseOnSep( std::string , std::string );
char string_to_char( std::string );
std::string strip( std::string );
#endif #endif
data/integrase.tsv.csv 100644 → 100755
View file @ 9a6ba918
#Integrase #integrase
Position Position AA Nucléotides CONCLUSION Position ,Position ,AA,Nucléotides,,CONCLUSION
AA nucléotides SAUVAGE AA FINAL AA,nucléotides,SAUVAGE,,AA FINAL,
49 145 A GCT A 49,145,A,GCT,A,
49 145 A GCC A WT 49,145,A,GCC,A,WT
49 145 A GCA A 49,145,A,GCA,A,
49 145 A GCG A 49,145,A,GCG,A,
49 145 A GGT G MUTE 49,145,A,GGT,G,MUTE
49 145 A GGC G MUTE 49,145,A,GGC,G,MUTE
49 145 A GGG G MUTE 49,145,A,GGG,G,MUTE
49 145 A GGA G MUTE 49,145,A,GGA,G,MUTE
66 196 T ACT T 66,196,T,ACT,T,
66 196 T ACC T 66,196,T,ACC,T,
66 196 T ACA T WT 66,196,T,ACA,T,WT
66 196 T ACG T 66,196,T,ACG,T,
66 196 T AAA K MUTE 66,196,T,AAA,K,MUTE
66 196 T AAG K MUTE 66,196,T,AAG,K,MUTE
66 196 T ATT I MUTE 66,196,T,ATT,I,MUTE
66 196 T ATC I MUTE 66,196,T,ATC,I,MUTE
66 196 T ATA I MUTE 66,196,T,ATA,I,MUTE
66 196 T GCT A MUTE 66,196,T,GCT,A,MUTE
66 196 T GCC A MUTE 66,196,T,GCC,A,MUTE
66 196 T GCA A MUTE 66,196,T,GCA,A,MUTE
66 196 T GCG A MUTE 66,196,T,GCG,A,MUTE
74 220 L TTG L 74,220,L,TTG,L,
74 220 L TTA L 74,220,L,TTA,L,
74 220 L CTT L 74,220,L,CTT,L,
74 220 L CTC L 74,220,L,CTC,L,
74 220 L CTG L WT 74,220,L,CTG,L,WT
74 220 L CTA L 74,220,L,CTA,L,
74 220 L ATT I MUTE 74,220,L,ATT,I,MUTE
74 220 L ATC I MUTE 74,220,L,ATC,I,MUTE
74 220 L ATA I MUTE 74,220,L,ATA,I,MUTE
74 220 L ATG M MUTE 74,220,L,ATG,M,MUTE
92 274 E GAA E WT 92,274,E,GAA,E,WT
92 274 E GAG E 92,274,E,GAG,E,
92 274 E CAA Q MUTE 92,274,E,CAA,Q,MUTE
92 274 E CAG Q MUTE 92,274,E,CAG,Q,MUTE
92 274 E GGA G MUTE 92,274,E,GGA,G,MUTE
92 274 E GGG G MUTE 92,274,E,GGG,G,MUTE
92 274 E GGT G MUTE 92,274,E,GGT,G,MUTE
92 274 E GGC G MUTE 92,274,E,GGC,G,MUTE
97 289 T ACT T 97,289,T,ACT,T,
97 289 T ACA T WT 97,289,T,ACA,T,WT
97 289 T ACG T 97,289,T,ACG,T,
97 289 T ACC T 97,289,T,ACC,T,
97 289 T GCA A MUTE 97,289,T,GCA,A,MUTE
97 289 T GCT A MUTE 97,289,T,GCT,A,MUTE
97 289 T GCG A MUTE 97,289,T,GCG,A,MUTE
97 289 T GCC A MUTE 97,289,T,GCC,A,MUTE
118 352 G GGT G 118,352,G,GGT,G,
118 352 G GGC G WT 118,352,G,GGC,G,WT
118 352 G GGA G 118,352,G,GGA,G,
118 352 G GGG G 118,352,G,GGG,G,
118 352 G CGT R MUTE 118,352,G,CGT,R,MUTE
118 352 G CGC R MUTE 118,352,G,CGC,R,MUTE
118 352 G CGA R MUTE 118,352,G,CGA,R,MUTE
118 352 G CGG R MUTE 118,352,G,CGG,R,MUTE
118 352 G AGA R MUTE 118,352,G,AGA,R,MUTE
118 352 G AGG R MUTE 118,352,G,AGG,R,MUTE
121 361 F TTT F 121,361,F,TTT,F,
121 361 F TTC F WT 121,361,F,TTC,F,WT
121 361 F TAT Y MUTE 121,361,F,TAT,Y,MUTE
121 361 F TAC Y MUTE 121,361,F,TAC,Y,MUTE
138 412 E GAA E WT 138,412,E,GAA,E,WT
138 412 E GAG E 138,412,E,GAG,E,
138 412 E AAA K MUTE 138,412,E,AAA,K,MUTE
138 412 E AAG K MUTE 138,412,E,AAG,K,MUTE
138 412 E GCT A MUTE 138,412,E,GCT,A,MUTE
138 412 E GCC A MUTE 138,412,E,GCC,A,MUTE
138 412 E GCA A MUTE 138,412,E,GCA,A,MUTE
138 412 E GCG A MUTE 138,412,E,GCG,A,MUTE
138 412 E ACT T MUTE 138,412,E,ACT,T,MUTE
138 412 E ACC T MUTE 138,412,E,ACC,T,MUTE
138 412 E ACA T MUTE 138,412,E,ACA,T,MUTE
138 412 E ACG T MUTE 138,412,E,ACG,T,MUTE
140 418 G GGT G 140,418,G,GGT,G,
140 418 G GGC G 140,418,G,GGC,G,
140 418 G GGA G WT 140,418,G,GGA,G,WT
140 418 G GGG G 140,418,G,GGG,G,
140 418 G GCT A MUTE 140,418,G,GCT,A,MUTE
140 418 G GCC A MUTE 140,418,G,GCC,A,MUTE
140 418 G GCA A MUTE 140,418,G,GCA,A,MUTE
140 418 G GCG A MUTE 140,418,G,GCG,A,MUTE
140 418 G TGT C MUTE 140,418,G,TGT,C,MUTE
140 418 G TGC C MUTE 140,418,G,TGC,C,MUTE
140 418 G TCT S MUTE 140,418,G,TCT,S,MUTE
140 418 G TCC S MUTE 140,418,G,TCC,S,MUTE
140 418 G TCA S MUTE 140,418,G,TCA,S,MUTE
140 418 G TCG S MUTE 140,418,G,TCG,S,MUTE
140 418 G AGT S MUTE 140,418,G,AGT,S,MUTE
140 418 G AGC S MUTE 140,418,G,AGC,S,MUTE
143 427 Y TAT Y 143,427,Y,TAT,Y,
143 427 Y TAC Y WT 143,427,Y,TAC,Y,WT
143 427 Y GCT A MUTE 143,427,Y,GCT,A,MUTE
143 427 Y GCC A MUTE 143,427,Y,GCC,A,MUTE
143 427 Y GCA A MUTE 143,427,Y,GCA,A,MUTE
143 427 Y GCG A MUTE 143,427,Y,GCG,A,MUTE
143 427 Y TGT C MUTE 143,427,Y,TGT,C,MUTE
143 427 Y TGC C MUTE 143,427,Y,TGC,C,MUTE
143 427 Y TCT S MUTE 143,427,Y,TCT,S,MUTE
143 427 Y TCC S MUTE 143,427,Y,TCC,S,MUTE
143 427 Y TCA S MUTE 143,427,Y,TCA,S,MUTE
143 427 Y TCG S MUTE 143,427,Y,TCG,S,MUTE
143 427 Y AGT S MUTE 143,427,Y,AGT,S,MUTE
143 427 Y AGC S MUTE 143,427,Y,AGC,S,MUTE
143 427 Y GGT G MUTE 143,427,Y,GGT,G,MUTE
143 427 Y GGC G MUTE 143,427,Y,GGC,G,MUTE
143 427 Y GGA G MUTE 143,427,Y,GGA,G,MUTE
143 427 Y GGG G MUTE 143,427,Y,GGG,G,MUTE
143 427 Y CAT H MUTE 143,427,Y,CAT,H,MUTE
143 427 Y CAC H MUTE 143,427,Y,CAC,H,MUTE
143 427 Y CGT R MUTE 143,427,Y,CGT,R,MUTE
143 427 Y CGC R MUTE 143,427,Y,CGC,R,MUTE
143 427 Y CGA R MUTE 143,427,Y,CGA,R,MUTE
143 427 Y CGG R MUTE 143,427,Y,CGG,R,MUTE
143 427 Y AGA R MUTE 143,427,Y,AGA,R,MUTE
143 427 Y AGG R MUTE 143,427,Y,AGG,R,MUTE
145 433 P CCT P 145,433,P,CCT,P,
145 433 P CCC P WT 145,433,P,CCC,P,WT
145 433 P CCA P 145,433,P,CCA,P,
145 433 P CCG P 145,433,P,CCG,P,
145 433 P TCC S MUTE 145,433,P,TCC,S,MUTE
145 433 P TCA S MUTE 145,433,P,TCA,S,MUTE
145 433 P TCG S MUTE 145,433,P,TCG,S,MUTE
145 433 P AGT S MUTE 145,433,P,AGT,S,MUTE
145 433 P AGC S MUTE 145,433,P,AGC,S,MUTE
145 433 P TCT S MUTE 145,433,P,TCT,S,MUTE
147 439 S TCT S 147,439,S,TCT,S,
147 439 S TCC S 147,439,S,TCC,S,
147 439 S TCA S 147,439,S,TCA,S,
147 439 S TCG S 147,439,S,TCG,S,
147 439 S AGT S WT 147,439,S,AGT,S,WT
147 439 S AGC S 147,439,S,AGC,S,
147 439 S GGT G MUTE 147,439,S,GGT,G,MUTE
147 439 S GGC G MUTE 147,439,S,GGC,G,MUTE
147 439 S GGA G MUTE 147,439,S,GGA,G,MUTE
147 439 S GGG G MUTE 147,439,S,GGG,G,MUTE
148 442 Q CAA Q WT 148,442,Q,CAA,Q,WT
148 442 Q CAG Q WT 148,442,Q,CAG,Q,WT
148 442 Q GAA E MUTE 148,442,Q,GAA,E,MUTE
148 442 Q GAG E MUTE 148,442,Q,GAG,E,MUTE
148 442 Q GGT G MUTE 148,442,Q,GGT,G,MUTE
148 442 Q GGT G MUTE 148,442,Q,GGT,G,MUTE
148 442 Q GGC G MUTE 148,442,Q,GGC,G,MUTE
148 442 Q GGA G MUTE 148,442,Q,GGA,G,MUTE
148 442 Q GGG G MUTE 148,442,Q,GGG,G,MUTE
148 442 Q CAC H MUTE 148,442,Q,CAC,H,MUTE
148 442 Q CAT H MUTE 148,442,Q,CAT,H,MUTE
148 442 Q AAA K MUTE 148,442,Q,AAA,K,MUTE
148 442 Q AAG K MUTE 148,442,Q,AAG,K,MUTE
148 442 Q CGA R MUTE 148,442,Q,CGA,R,MUTE
148 442 Q CGG R MUTE 148,442,Q,CGG,R,MUTE
148 442 Q AGA R MUTE 148,442,Q,AGA,R,MUTE
148 442 Q AGG R MUTE 148,442,Q,AGG,R,MUTE
151 451 V GTT V 151,451,V,GTT,V,
151 451 V GTC V 151,451,V,GTC,V,
151 451 V GTA V WT 151,451,V,GTA,V,WT
151 451 V GTG V 151,451,V,GTG,V,
151 451 V TTG L MUTE 151,451,V,TTG,L,MUTE
151 451 V TTA L MUTE 151,451,V,TTA,L,MUTE
151 451 V CTT L MUTE 151,451,V,CTT,L,MUTE
151 451 V CTC L MUTE 151,451,V,CTC,L,MUTE
151 451 V CTG L MUTE 151,451,V,CTG,L,MUTE
151 451 V CTA L MUTE 151,451,V,CTA,L,MUTE
153 457 S TCT S WT 153,457,S,TCT,S,WT
153 457 S TCC S 153,457,S,TCC,S,
153 457 S TCA S 153,457,S,TCA,S,
153 457 S TCG S 153,457,S,TCG,S,
153 457 S AGT S 153,457,S,AGT,S,
153 457 S AGC S 153,457,S,AGC,S,
153 457 S TTT F MUTE 153,457,S,TTT,F,MUTE
153 457 S TTC F MUTE 153,457,S,TTC,F,MUTE
153 457 S TAT Y MUTE 153,457,S,TAT,Y,MUTE
153 457 S TAC Y MUTE 153,457,S,TAC,Y,MUTE
155 463 N AAT N WT 155,463,N,AAT,N,WT
155 463 N AAC N 155,463,N,AAC,N,
155 463 N CAT H MUTE 155,463,N,CAT,H,MUTE
155 463 N CAC H MUTE 155,463,N,CAC,H,MUTE
155 463 N TCC S MUTE 155,463,N,TCC,S,MUTE
155 463 N TCA S MUTE 155,463,N,TCA,S,MUTE
155 463 N TCG S MUTE 155,463,N,TCG,S,MUTE
155 463 N AGT S MUTE 155,463,N,AGT,S,MUTE
155 463 N AGC S MUTE 155,463,N,AGC,S,MUTE
155 463 N TCT S MUTE 155,463,N,TCT,S,MUTE
155 463 N ACT T MUTE 155,463,N,ACT,T,MUTE
155 463 N ACC T MUTE 155,463,N,ACC,T,MUTE
155 463 N ACA T MUTE 155,463,N,ACA,T,MUTE
155 463 N ACG T MUTE 155,463,N,ACG,T,MUTE
157 469 E GAA E WT 157,469,E,GAA,E,WT
157 469 E GAG E 157,469,E,GAG,E,
157 469 E CAA Q MUTE 157,469,E,CAA,Q,MUTE
157 469 E CAG Q MUTE 157,469,E,CAG,Q,MUTE
230 688 S TCT S 230,688,S,TCT,S,
230 688 S TCC S 230,688,S,TCC,S,
230 688 S TCA S 230,688,S,TCA,S,
230 688 S TCG S 230,688,S,TCG,S,
230 688 S AGT S 230,688,S,AGT,S,
230 688 S AGC S WT 230,688,S,AGC,S,WT
230 688 S GGT G MUTE 230,688,S,GGT,G,MUTE
230 688 S GGC G MUTE 230,688,S,GGC,G,MUTE
230 688 S GGA G MUTE 230,688,S,GGA,G,MUTE
230 688 S GGG G MUTE 230,688,S,GGG,G,MUTE
230 688 S CGA R MUTE 230,688,S,CGA,R,MUTE
230 688 S CGG R MUTE 230,688,S,CGG,R,MUTE
230 688 S AGA R MUTE 230,688,S,AGA,R,MUTE
230 688 S AGG R MUTE 230,688,S,AGG,R,MUTE
263 787 R AGG R 263,787,R,AGG,R,
263 787 R AGA R WT 263,787,R,AGA,R,WT
263 787 R AAA K MUTE 263,787,R,AAA,K,MUTE
263 787 R AAG K MUTE 263,787,R,AAG,K,MUTE
data/protease.tsv.csv 100644 → 100755
View file @ 9a6ba918
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data/reversetranscriptase.tsv.csv 100644 → 100755
View file @ 9a6ba918
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