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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 227 additions and 222 deletions
cpp/utils.h 100644 → 100755
View file @ 9a6ba918
#ifndef _UTILS_H
#define _UTILS_H
#include <vector>
bool IsFileReadable( std::string );
void ExecMeasure( struct timeval, struct timeval, std::string );
......@@ -10,5 +12,8 @@ std::string int_to_string( int );
char checkBase(char);
std::string pyReplace( std::string , std::string , std::string );
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
data/integrase.tsv.csv 100644 → 100755
View file @ 9a6ba918
#Integrase
Position Position AA Nucléotides CONCLUSION
AA nucléotides SAUVAGE AA FINAL
49 145 A GCT A
49 145 A GCC A WT
49 145 A GCA A
49 145 A GCG A
49 145 A GGT G MUTE
49 145 A GGC G MUTE
49 145 A GGG G MUTE
49 145 A GGA G MUTE
66 196 T ACT T
66 196 T ACC T
66 196 T ACA T WT
66 196 T ACG T
66 196 T AAA K MUTE
66 196 T AAG K MUTE
66 196 T ATT I MUTE
66 196 T ATC I MUTE
66 196 T ATA I MUTE
66 196 T GCT A MUTE
66 196 T GCC A MUTE
66 196 T GCA A MUTE
66 196 T GCG A MUTE
74 220 L TTG L
74 220 L TTA L
74 220 L CTT L
74 220 L CTC L
74 220 L CTG L WT
74 220 L CTA L
74 220 L ATT I MUTE
74 220 L ATC I MUTE
74 220 L ATA I MUTE
74 220 L ATG M MUTE
92 274 E GAA E WT
92 274 E GAG E
92 274 E CAA Q MUTE
92 274 E CAG Q MUTE
92 274 E GGA G MUTE
92 274 E GGG G MUTE
92 274 E GGT G MUTE
92 274 E GGC G MUTE
97 289 T ACT T
97 289 T ACA T WT
97 289 T ACG T
97 289 T ACC T
97 289 T GCA A MUTE
97 289 T GCT A MUTE
97 289 T GCG A MUTE
97 289 T GCC A MUTE
118 352 G GGT G
118 352 G GGC G WT
118 352 G GGA G
118 352 G GGG G
118 352 G CGT R MUTE
118 352 G CGC R MUTE
118 352 G CGA R MUTE
118 352 G CGG R MUTE
118 352 G AGA R MUTE
118 352 G AGG R MUTE
121 361 F TTT F
121 361 F TTC F WT
121 361 F TAT Y MUTE
121 361 F TAC Y MUTE
138 412 E GAA E WT
138 412 E GAG E
138 412 E AAA K MUTE
138 412 E AAG K MUTE
138 412 E GCT A MUTE
138 412 E GCC A MUTE
138 412 E GCA A MUTE
138 412 E GCG A MUTE
138 412 E ACT T MUTE
138 412 E ACC T MUTE
138 412 E ACA T MUTE
138 412 E ACG T MUTE
140 418 G GGT G
140 418 G GGC G
140 418 G GGA G WT
140 418 G GGG G
140 418 G GCT A MUTE
140 418 G GCC A MUTE
140 418 G GCA A MUTE
140 418 G GCG A MUTE
140 418 G TGT C MUTE
140 418 G TGC C MUTE
140 418 G TCT S MUTE
140 418 G TCC S MUTE
140 418 G TCA S MUTE
140 418 G TCG S MUTE
140 418 G AGT S MUTE
140 418 G AGC S MUTE
143 427 Y TAT Y
143 427 Y TAC Y WT
143 427 Y GCT A MUTE
143 427 Y GCC A MUTE
143 427 Y GCA A MUTE
143 427 Y GCG A MUTE
143 427 Y TGT C MUTE
143 427 Y TGC C MUTE
143 427 Y TCT S MUTE
143 427 Y TCC S MUTE
143 427 Y TCA S MUTE
143 427 Y TCG S MUTE
143 427 Y AGT S MUTE
143 427 Y AGC S MUTE
143 427 Y GGT G MUTE
143 427 Y GGC G MUTE
143 427 Y GGA G MUTE
143 427 Y GGG G MUTE
143 427 Y CAT H MUTE
143 427 Y CAC H MUTE
143 427 Y CGT R MUTE
143 427 Y CGC R MUTE
143 427 Y CGA R MUTE
143 427 Y CGG R MUTE
143 427 Y AGA R MUTE
143 427 Y AGG R MUTE
145 433 P CCT P
145 433 P CCC P WT
145 433 P CCA P
145 433 P CCG P
145 433 P TCC S MUTE
145 433 P TCA S MUTE
145 433 P TCG S MUTE
145 433 P AGT S MUTE
145 433 P AGC S MUTE
145 433 P TCT S MUTE
147 439 S TCT S
147 439 S TCC S
147 439 S TCA S
147 439 S TCG S
147 439 S AGT S WT
147 439 S AGC S
147 439 S GGT G MUTE
147 439 S GGC G MUTE
147 439 S GGA G MUTE
147 439 S GGG G MUTE
148 442 Q CAA Q WT
148 442 Q CAG Q WT
148 442 Q GAA E MUTE
148 442 Q GAG E MUTE
148 442 Q GGT G MUTE
148 442 Q GGT G MUTE
148 442 Q GGC G MUTE
148 442 Q GGA G MUTE
148 442 Q GGG G MUTE
148 442 Q CAC H MUTE
148 442 Q CAT H MUTE
148 442 Q AAA K MUTE
148 442 Q AAG K MUTE
148 442 Q CGA R MUTE
148 442 Q CGG R MUTE
148 442 Q AGA R MUTE
148 442 Q AGG R MUTE
151 451 V GTT V
151 451 V GTC V
151 451 V GTA V WT
151 451 V GTG V
151 451 V TTG L MUTE
151 451 V TTA L MUTE
151 451 V CTT L MUTE
151 451 V CTC L MUTE
151 451 V CTG L MUTE
151 451 V CTA L MUTE
153 457 S TCT S WT
153 457 S TCC S
153 457 S TCA S
153 457 S TCG S
153 457 S AGT S
153 457 S AGC S
153 457 S TTT F MUTE
153 457 S TTC F MUTE
153 457 S TAT Y MUTE
153 457 S TAC Y MUTE
155 463 N AAT N WT
155 463 N AAC N
155 463 N CAT H MUTE
155 463 N CAC H MUTE
155 463 N TCC S MUTE
155 463 N TCA S MUTE
155 463 N TCG S MUTE
155 463 N AGT S MUTE
155 463 N AGC S MUTE
155 463 N TCT S MUTE
155 463 N ACT T MUTE
155 463 N ACC T MUTE
155 463 N ACA T MUTE
155 463 N ACG T MUTE
157 469 E GAA E WT
157 469 E GAG E
157 469 E CAA Q MUTE
157 469 E CAG Q MUTE
230 688 S TCT S
230 688 S TCC S
230 688 S TCA S
230 688 S TCG S
230 688 S AGT S
230 688 S AGC S WT
230 688 S GGT G MUTE
230 688 S GGC G MUTE
230 688 S GGA G MUTE
230 688 S GGG G MUTE
230 688 S CGA R MUTE
230 688 S CGG R MUTE
230 688 S AGA R MUTE
230 688 S AGG R MUTE
263 787 R AGG R
263 787 R AGA R WT
263 787 R AAA K MUTE
263 787 R AAG K MUTE
#integrase
Position ,Position ,AA,Nucléotides,,CONCLUSION
AA,nucléotides,SAUVAGE,,AA FINAL,
49,145,A,GCT,A,
49,145,A,GCC,A,WT
49,145,A,GCA,A,
49,145,A,GCG,A,
49,145,A,GGT,G,MUTE
49,145,A,GGC,G,MUTE
49,145,A,GGG,G,MUTE
49,145,A,GGA,G,MUTE
66,196,T,ACT,T,
66,196,T,ACC,T,
66,196,T,ACA,T,WT
66,196,T,ACG,T,
66,196,T,AAA,K,MUTE
66,196,T,AAG,K,MUTE
66,196,T,ATT,I,MUTE
66,196,T,ATC,I,MUTE
66,196,T,ATA,I,MUTE
66,196,T,GCT,A,MUTE
66,196,T,GCC,A,MUTE
66,196,T,GCA,A,MUTE
66,196,T,GCG,A,MUTE
74,220,L,TTG,L,
74,220,L,TTA,L,
74,220,L,CTT,L,
74,220,L,CTC,L,
74,220,L,CTG,L,WT
74,220,L,CTA,L,
74,220,L,ATT,I,MUTE
74,220,L,ATC,I,MUTE
74,220,L,ATA,I,MUTE
74,220,L,ATG,M,MUTE
92,274,E,GAA,E,WT
92,274,E,GAG,E,
92,274,E,CAA,Q,MUTE
92,274,E,CAG,Q,MUTE
92,274,E,GGA,G,MUTE
92,274,E,GGG,G,MUTE
92,274,E,GGT,G,MUTE
92,274,E,GGC,G,MUTE
97,289,T,ACT,T,
97,289,T,ACA,T,WT
97,289,T,ACG,T,
97,289,T,ACC,T,
97,289,T,GCA,A,MUTE
97,289,T,GCT,A,MUTE
97,289,T,GCG,A,MUTE
97,289,T,GCC,A,MUTE
118,352,G,GGT,G,
118,352,G,GGC,G,WT
118,352,G,GGA,G,
118,352,G,GGG,G,
118,352,G,CGT,R,MUTE
118,352,G,CGC,R,MUTE
118,352,G,CGA,R,MUTE
118,352,G,CGG,R,MUTE
118,352,G,AGA,R,MUTE
118,352,G,AGG,R,MUTE
121,361,F,TTT,F,
121,361,F,TTC,F,WT
121,361,F,TAT,Y,MUTE
121,361,F,TAC,Y,MUTE
138,412,E,GAA,E,WT
138,412,E,GAG,E,
138,412,E,AAA,K,MUTE
138,412,E,AAG,K,MUTE
138,412,E,GCT,A,MUTE
138,412,E,GCC,A,MUTE
138,412,E,GCA,A,MUTE
138,412,E,GCG,A,MUTE
138,412,E,ACT,T,MUTE
138,412,E,ACC,T,MUTE
138,412,E,ACA,T,MUTE
138,412,E,ACG,T,MUTE
140,418,G,GGT,G,
140,418,G,GGC,G,
140,418,G,GGA,G,WT
140,418,G,GGG,G,
140,418,G,GCT,A,MUTE
140,418,G,GCC,A,MUTE
140,418,G,GCA,A,MUTE
140,418,G,GCG,A,MUTE
140,418,G,TGT,C,MUTE
140,418,G,TGC,C,MUTE
140,418,G,TCT,S,MUTE
140,418,G,TCC,S,MUTE
140,418,G,TCA,S,MUTE
140,418,G,TCG,S,MUTE
140,418,G,AGT,S,MUTE
140,418,G,AGC,S,MUTE
143,427,Y,TAT,Y,
143,427,Y,TAC,Y,WT
143,427,Y,GCT,A,MUTE
143,427,Y,GCC,A,MUTE
143,427,Y,GCA,A,MUTE
143,427,Y,GCG,A,MUTE
143,427,Y,TGT,C,MUTE
143,427,Y,TGC,C,MUTE
143,427,Y,TCT,S,MUTE
143,427,Y,TCC,S,MUTE
143,427,Y,TCA,S,MUTE
143,427,Y,TCG,S,MUTE
143,427,Y,AGT,S,MUTE
143,427,Y,AGC,S,MUTE
143,427,Y,GGT,G,MUTE
143,427,Y,GGC,G,MUTE
143,427,Y,GGA,G,MUTE
143,427,Y,GGG,G,MUTE
143,427,Y,CAT,H,MUTE
143,427,Y,CAC,H,MUTE
143,427,Y,CGT,R,MUTE
143,427,Y,CGC,R,MUTE
143,427,Y,CGA,R,MUTE
143,427,Y,CGG,R,MUTE
143,427,Y,AGA,R,MUTE
143,427,Y,AGG,R,MUTE
145,433,P,CCT,P,
145,433,P,CCC,P,WT
145,433,P,CCA,P,
145,433,P,CCG,P,
145,433,P,TCC,S,MUTE
145,433,P,TCA,S,MUTE
145,433,P,TCG,S,MUTE
145,433,P,AGT,S,MUTE
145,433,P,AGC,S,MUTE
145,433,P,TCT,S,MUTE
147,439,S,TCT,S,
147,439,S,TCC,S,
147,439,S,TCA,S,
147,439,S,TCG,S,
147,439,S,AGT,S,WT
147,439,S,AGC,S,
147,439,S,GGT,G,MUTE
147,439,S,GGC,G,MUTE
147,439,S,GGA,G,MUTE
147,439,S,GGG,G,MUTE
148,442,Q,CAA,Q,WT
148,442,Q,CAG,Q,WT
148,442,Q,GAA,E,MUTE
148,442,Q,GAG,E,MUTE
148,442,Q,GGT,G,MUTE
148,442,Q,GGT,G,MUTE
148,442,Q,GGC,G,MUTE
148,442,Q,GGA,G,MUTE
148,442,Q,GGG,G,MUTE
148,442,Q,CAC,H,MUTE
148,442,Q,CAT,H,MUTE
148,442,Q,AAA,K,MUTE
148,442,Q,AAG,K,MUTE
148,442,Q,CGA,R,MUTE
148,442,Q,CGG,R,MUTE
148,442,Q,AGA,R,MUTE
148,442,Q,AGG,R,MUTE
151,451,V,GTT,V,
151,451,V,GTC,V,
151,451,V,GTA,V,WT
151,451,V,GTG,V,
151,451,V,TTG,L,MUTE
151,451,V,TTA,L,MUTE
151,451,V,CTT,L,MUTE
151,451,V,CTC,L,MUTE
151,451,V,CTG,L,MUTE
151,451,V,CTA,L,MUTE
153,457,S,TCT,S,WT
153,457,S,TCC,S,
153,457,S,TCA,S,
153,457,S,TCG,S,
153,457,S,AGT,S,
153,457,S,AGC,S,
153,457,S,TTT,F,MUTE
153,457,S,TTC,F,MUTE
153,457,S,TAT,Y,MUTE
153,457,S,TAC,Y,MUTE
155,463,N,AAT,N,WT
155,463,N,AAC,N,
155,463,N,CAT,H,MUTE
155,463,N,CAC,H,MUTE
155,463,N,TCC,S,MUTE
155,463,N,TCA,S,MUTE
155,463,N,TCG,S,MUTE
155,463,N,AGT,S,MUTE
155,463,N,AGC,S,MUTE
155,463,N,TCT,S,MUTE
155,463,N,ACT,T,MUTE
155,463,N,ACC,T,MUTE
155,463,N,ACA,T,MUTE
155,463,N,ACG,T,MUTE
157,469,E,GAA,E,WT
157,469,E,GAG,E,
157,469,E,CAA,Q,MUTE
157,469,E,CAG,Q,MUTE
230,688,S,TCT,S,
230,688,S,TCC,S,
230,688,S,TCA,S,
230,688,S,TCG,S,
230,688,S,AGT,S,
230,688,S,AGC,S,WT
230,688,S,GGT,G,MUTE
230,688,S,GGC,G,MUTE
230,688,S,GGA,G,MUTE
230,688,S,GGG,G,MUTE
230,688,S,CGA,R,MUTE
230,688,S,CGG,R,MUTE
230,688,S,AGA,R,MUTE
230,688,S,AGG,R,MUTE
263,787,R,AGG,R,
263,787,R,AGA,R,WT
263,787,R,AAA,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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