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jpayne@69
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1 #include "translate.hh"
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2
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3
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4 long int Translate_DNA
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5 (char * A, char * tA, int Frame)
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6
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7 // function to translate dna sequence to aminoacid sequence
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8 // uses esttrans' headers and algo
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9 // A as read in from gene.h Read_String
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10 // tA should be an empty string malloced to atleast (Len A / 3)
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11 // frame is 1,2,3,4,5,6
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12 // returns new (strlen(tA+1)) or -1 on error
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13
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14 {
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15 int dna_int;
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16 int dnaseq_len, aaseq_len;
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17 int aa_index;
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18 char *dna_seq, *dna_ptr, *dna_end, *aa_ptr;
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19
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20 dnaseq_len = strlen ( A + 1 );
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21 aa_ptr = tA + 1;
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22 dna_seq = A + 1;
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23 dna_end = A + dnaseq_len;
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24
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25 if ( Frame >= 1 && Frame <= 3 )
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26 {
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27 dna_end -= 2;
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28 dna_ptr = dna_seq + Frame - 1;
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29 for (; dna_ptr <= dna_end;)
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30 {
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31 dna_int = transdna [ int(*dna_ptr++) ];
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32 if ( dna_int == BAD_PEP_CHAR ) {
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33 fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
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34 dna_int = DNA_XN;
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35 }
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36 aa_index = dna_int;
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37 aa_index <<= 4;
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38
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39 dna_int = transdna [ int(*dna_ptr++) ];
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40 if ( dna_int == BAD_PEP_CHAR ) {
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41 fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
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42 dna_int = DNA_XN;
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43 }
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44 aa_index += dna_int;
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45 aa_index <<= 4;
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46
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47 dna_int = transdna [ int(*dna_ptr++) ];
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48 if ( dna_int == BAD_PEP_CHAR ) {
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49 fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
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50 dna_int = DNA_XN;
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51 }
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52 aa_index += dna_int;
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53
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54 *(aa_ptr++) = universal[aa_index];
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55 }
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56
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57 *aa_ptr = '\0';
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58 aaseq_len = strlen ( tA + 1 );
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59 }
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60 else if ( Frame >= 4 && Frame <= 6 )
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61 {
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62 Frame -= 3;
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63
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64 dna_seq += 2;
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65 dna_ptr = dna_end - Frame + 1;
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66 for (; dna_ptr >= dna_seq;)
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67 {
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68 dna_int = compdna [ transdna [ int(*dna_ptr--)] ];
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69 if ( dna_int == BAD_PEP_CHAR ) {
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70 fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
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71 dna_int = DNA_XN;
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72 }
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73 aa_index = dna_int;
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74 aa_index <<= 4;
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75
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76 dna_int = compdna [ transdna [ int(*dna_ptr--)] ];
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77 if ( dna_int == BAD_PEP_CHAR ) {
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78 fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
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79 dna_int = DNA_XN;
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80 }
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81 aa_index += dna_int;
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82 aa_index <<= 4;
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83
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84 dna_int = compdna [ transdna [ int(*dna_ptr--)] ];
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85 if ( dna_int == BAD_PEP_CHAR ) {
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86 fprintf(stderr,"WARNING: Forcing unrecognized DNA char to N\n");
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87 dna_int = DNA_XN;
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88 }
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89 aa_index += dna_int;
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90
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91 *(aa_ptr++) = universal[aa_index];
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92 }
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93
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94 *aa_ptr = '\0';
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95 aaseq_len = strlen ( tA + 1 );
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96 }
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97 else
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98 aaseq_len = -1;
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99
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100
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101 return aaseq_len;
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102 }
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103
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