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/* routines for handling the genetic code
We need to be able to have a standard code and allow changes
to make a current code.
We need to translate dna to amino acids.
We need to count codons.
We need to use indexes into the codon tables for several methods.
The genetic code is written tcag order, our lookups are acgt.
*/
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include "dna_utils.h"
/* #include "readpam.h" */
/************************************************************/
char genetic_code [5][5][5] = {
'F','F','L','L','-',
'S','S','S','S','S',
'Y','Y','*','*','-',
'C','C','*','W','-',
'-','-','-','-','-',
'L','L','L','L','L',
'P','P','P','P','P',
'H','H','Q','Q','-',
'R','R','R','R','R',
'-','-','-','-','-',
'I','I','I','M','-',
'T','T','T','T','T',
'N','N','K','K','-',
'S','S','R','R','-',
'-','-','-','-','-',
'V','V','V','V','V',
'A','A','A','A','A',
'D','D','E','E','-',
'G','G','G','G','G',
'-','-','-','-','-',
'-','-','-','-','-',
'-','-','-','-','-',
'-','-','-','-','-',
'-','-','-','-','-',
'-','-','-','-','-'
};
int genetic_code_index[5] = {2,1,3,0,4};
int cgenetic_code_index[5] = {0,3,1,2,4};
char *three_letter_code ( char one_letter_code ) {
/* Input character representing an amino acid in 1 letter code
Output its three letter code equivalent
Note we assume incoming character is upper case
*/
char one_letter[] = {"ACDEFGHIKLMNPQRSTVWY*-"};
char *three_letter[] = {
"Ala","Cys","Asp","Glu","Phe","Gly","His","Ile","Lys",
"Leu","Met","Asn","Pro","Gln","Arg","Ser","Thr","Val",
"Trp","Tyr","***","---"};
int i;
one_letter_code = toupper(one_letter_code);
for (i=0;i<sizeof(one_letter)-1;i++){
if ( one_letter_code == one_letter[i] ) return three_letter[i];
}
return " ";
}
/************************************************************/
int codon_table_index ( char *codon ) {
/* given a codon of three bases, return an index into
a 64 element codon table */
/* check for illegal symbol. If found return 64 Calling routines please note*/
int i;
for(i=0;i<3;i++) {
if ( dna_lookup [ codon [ i ] ] == 4 ) return 64;
}
return genetic_code_index [ dna_lookup [ codon [ 0 ] ] ] |
(genetic_code_index [ dna_lookup [ codon [ 1 ] ] ]) <<2 |
(genetic_code_index [ dna_lookup [ codon [ 2 ] ] ]) <<4;
}
/************************************************************/
char codon_to_acid1 ( char *codon ) {
/* given a codon of three bases, return the one letter code for the acid */
return genetic_code [ genetic_code_index [ dna_lookup [ codon [ 0 ] ] ] ]
[ genetic_code_index [ dna_lookup [ codon [ 1 ] ] ] ]
[ genetic_code_index [ dna_lookup [ codon [ 2 ] ] ] ];
}
/************************************************************/
char codon_to_cacid1 ( char *codon ) {
/* given a codon of three bases, return the one letter code for the acid
on the complementary strand */
return genetic_code [ cgenetic_code_index [ dna_lookup [ codon [ 2 ] ] ] ]
[ cgenetic_code_index [ dna_lookup [ codon [ 1 ] ] ] ]
[ cgenetic_code_index [ dna_lookup [ codon [ 0 ] ] ] ];
}
/************************************************************/
char *codon_to_acid3 ( char *codon ) {
/* given a codon of three bases, return the three letter code for the acid */
char c;
c = genetic_code [ genetic_code_index [ dna_lookup [ codon [ 0 ] ] ] ]
[ genetic_code_index [ dna_lookup [ codon [ 1 ] ] ] ]
[ genetic_code_index [ dna_lookup [ codon [ 2 ] ] ] ];
return three_letter_code(c);
}
/************************************************************/
char *codon_to_cacid3 ( char *codon ) {
/* given a codon of three bases, return the three letter code for the acid */
char c;
c = genetic_code [ cgenetic_code_index [ dna_lookup [ codon [ 2 ] ] ] ]
[ cgenetic_code_index [ dna_lookup [ codon [ 1 ] ] ] ]
[ cgenetic_code_index [ dna_lookup [ codon [ 0 ] ] ] ];
return three_letter_code(c);
}
/************************************************************/
int read_codon_table ( FILE *in_file, double codon_table[4][4][4] ) {
/* read in a codon table */
int i,k;
char line[60];
/*
12345678901234567890123456789012345678901234567890
===========================================
F TTT 17. S TCT 16. Y TAT 10. C TGT 2.
F TTC 3. S TCC 6. Y TAC 0. C TGC 0.
L TTA 11. S TCA 6. * TAA 1. * TGA 2.
L TTG 8. S TCG 2. * TAG 0. W TGG 6.
===========================================
L CTT 7. P CCT 5. H CAT 4. R CGT 8.
L CTC 5. P CCC 2. H CAC 3. R CGC 4.
L CTA 2. P CCA 3. Q CAA 7. R CGA 3.
L CTG 7. P CCG 1. Q CAG 7. R CGG 1.
===========================================
I ATT 12. T ACT 10. N AAT 18. S AGT 3.
I ATC 4. T ACC 4. N AAC 4. S AGC 4.
I ATA 1. T ACA 1. K AAA 13. R AGA 3.
M ATG 7. T ACG 2. K AAG 7. R AGG 1.
===========================================
V GTT 14. A GCT 8. D GAT 7. G GGT 7.
V GTC 2. A GCC 3. D GAC 7. G GGC 1.
V GTA 7. A GCA 9. E GAA 6. G GGA 0.
V GTG 1. A GCG 0. E GAG 6. G GGG 2.
===========================================
012345678901234567890123456789012345678901234567890
*/
for(i=0;i<4;i++) {
if (fgets(line,55,in_file) == NULL ) return 0;
for(k=0;k<4;k++) {
if (fgets(line,55,in_file) == NULL ) return 0;
line[17] = line[28] = line[39] = line[50] = '\0';
codon_table[i][0][k] = atof(&line[11]);
codon_table[i][1][k] = atof(&line[22]);
codon_table[i][2][k] = atof(&line[33]);
codon_table[i][3][k] = atof(&line[44]);
}
}
return 1;
}
/************************************************************/
int write_codon_table ( FILE *out_file, double codon_table[4][4][4] ) {
/* write out a codon table */
int i,k;
char bases[] = {"tcag"};
/*
12345678901234567890123456789012345678901234567890
===========================================
F TTT 17. S TCT 16. Y TAT 10. C TGT 2.
F TTC 3. S TCC 6. Y TAC 0. C TGC 0.
L TTA 11. S TCA 6. * TAA 1. * TGA 2.
L TTG 8. S TCG 2. * TAG 0. W TGG 6.
===========================================
L CTT 7. P CCT 5. H CAT 4. R CGT 8.
L CTC 5. P CCC 2. H CAC 3. R CGC 4.
L CTA 2. P CCA 3. Q CAA 7. R CGA 3.
L CTG 7. P CCG 1. Q CAG 7. R CGG 1.
===========================================
I ATT 12. T ACT 10. N AAT 18. S AGT 3.
I ATC 4. T ACC 4. N AAC 4. S AGC 4.
I ATA 1. T ACA 1. K AAA 13. R AGA 3.
M ATG 7. T ACG 2. K AAG 7. R AGG 1.
===========================================
V GTT 14. A GCT 8. D GAT 7. G GGT 7.
V GTC 2. A GCC 3. D GAC 7. G GGC 1.
V GTA 7. A GCA 9. E GAA 6. G GGA 0.
V GTG 1. A GCG 0. E GAG 6. G GGG 2.
===========================================
01234567890123456789012345678901234567890123456789012
===============================================
F ttt 17 S tct 16 Y tat 10 C tgt 2
L ttc 3 P tcc 6 H tac 0 R tgc 0
I tta 11 T tca 6 N taa 1 S tga 2
V ttg 8 A tcg 2 D tag 0 G tgg 6
===============================================
F ctt 7 S cct 5 Y cat 4 C cgt 8
L ctc 5 P ccc 2 H cac 3 R cgc 4
I cta 2 T cca 3 N caa 7 S cga 3
V ctg 7 A ccg 1 D cag 7 G cgg 1
===============================================
L att 12 S act 10 * aat 18 * agt 3
L atc 4 P acc 4 Q aac 4 R agc 4
I ata 1 T aca 1 K aaa 13 R aga 3
V atg 7 A acg 2 E aag 7 G agg 1
===============================================
L gtt 14 S gct 8 * gat 7 W ggt 7
L gtc 2 P gcc 3 Q gac 7 R ggc 1
M gta 7 T gca 9 K gaa 6 R gga 0
V gtg 1 A gcg 0 E gag 6 G ggg 2
===============================================
12345678901234567890123456789012345678901234567890123
*/
for(i=0;i<4;i++) {
fprintf(out_file," ===============================================\n");
for(k=0;k<4;k++) {
fprintf(out_file," %c %c%c%c%6.0f %c %c%c%c%6.0f %c %c%c%c%6.0f %c %c%c%c%6.0f\n",
genetic_code[k][0][i],bases[i],bases[0],bases[k],
codon_table[i][0][k],
genetic_code[k][1][i],bases[i],bases[1],bases[k],
codon_table[i][1][k],
genetic_code[k][2][i],bases[i],bases[2],bases[k],
codon_table[i][2][k],
genetic_code[k][3][i],bases[i],bases[3],bases[k],
codon_table[i][3][k]);
}
}
fprintf(out_file," ===============================================\n");
return 1;
}
/************************************************************/
void zero_codon_table ( double codon_table[4][4][4] ) {
/* zero a codon table */
int i,j,k;
for(i=0;i<4;i++) {
for(j=0;j<4;j++) {
for(k=0;k<4;k++) {
codon_table[i][j][k] = 0.0;
}
}
}
}
/************************************************************/
#if 0
main() {
char seq[] = "aatgctcgataggctcgtatatgcgcgctattatatatgcgcg";
char codon[] = {'t','c','a'};
int i;
double codon_table[4][4][4];
FILE *in_file;
char *file_name = "codon_table";
in_file = fopen(file_name,"r");
i = read_codon_table(in_file,codon_table);
i = write_codon_table(stdout,codon_table);
(void) zero_codon_table(codon_table);
i = write_codon_table(stdout,codon_table);
sbl();
/* codon[1] = 't';
codon[2] = 't';*/
codon[0] = 'g';
codon[1] = 'g';
codon[2] = 'g';
printf(" index %d\n",codon_table_index(codon));
printf("tca %c\n",acid_from_codon(codon));
printf("tca %c\n",cacid_from_codon(codon));
codon[0] = 'a';
printf("tca %c\n",cacid_from_codon(codon));
codon[1] = 'a';
printf("tca %c\n",cacid_from_codon(codon));
printf("%c\n",genetic_code[1][2][3]);
printf("%c\n",genetic_code[0][1][4]);
printf("%c\n",genetic_code
[genetic_code_index[1]]
[genetic_code_index[2]]
[genetic_code_index[3]]);
printf("%s\n",three_letter_code('W'));
printf("%d %d %d\n",strlen(seq),3*strlen(seq),3*(strlen(seq)/3));
for(i=0;i<3*(strlen(seq)/3);i+=3) {
printf("%s",three_letter_codon(&seq[i]));
}
printf("\n");
for(i=0;i<3*(strlen(seq)/3);i+=3) {
printf("%c ",acid_from_codon(&seq[i]));
}
printf("\n");
}
#endif
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