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annotate consensus.c @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #include <stdio.h>
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2 #include <stdlib.h>
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3 #include <string.h>
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4 #include <ctype.h>
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5 #include <limits.h>
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6
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7 // N.B. This defines the valid bases, but it's also effectively defined in the switches in
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8 // get_votes_simple(), get_votes_qual(), and get_base_prime(), and in the constant IUPAC_BASES.
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9 #define N_BASES 6
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10 const char *BASES = "ACGTN-";
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11 /* A C G T N - A: 2 Compute IUPAC ambiguous base character by representing each base
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12 A 4 6 10 14 22 26 C: 3 with a prime and multiplying. Then use a lookup table (an array
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13 C 9 15 21 33 39 G: 5 where the index is the product of the two primes).
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14 G 25 35 55 65 T: 7
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15 T 49 77 91 N: 11
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16 N 121 143 -: 13 1 2 3 4 5 6 7
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17 - 169 01234567890123456789012345678901234567890123456789012345678901234567890*/
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18 const char *IUPAC_BASES = "N...A.M..CR...WS.....YN..GN......N.K...N.........T.....N.........N....."
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19 // 8 9 10 11 12 13 14
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20 "......N.............N.............................N..................."
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21 // 15 16 17
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22 "..N.........................-";
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23 #define THRES_DEFAULT 0.5
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24 #define WIN_LEN 4
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25 #define GAP_CHAR ' '
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26
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27 int **get_votes_simple(char *align[], int n_seqs, int seq_len);
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28 int **get_votes_qual(char *align[], char *quals[], int n_seqs, int seq_len, char thres);
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29 int init_gap_qual_window(int *window, char *quals, int seq_len);
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30 char get_gap_qual(int *window);
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31 int push_qual(int *window, int win_edge, char *quals, int seq_len);
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32 void print_window(int *window, int win_edge);
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33 int **init_votes(int seq_len);
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34 void free_votes(int *votes[], int seq_len);
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35 void print_votes(char *consensus, int *votes[], int seq_len);
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36 char *rm_gaps(char *consensus, int cons_len);
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37 char *build_consensus(int *votes[], int seq_len, double thres);
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38 char *build_consensus_duplex(int *votes1[], int *votes2[], int seq_len, double thres);
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39 char *build_consensus_duplex_simple(char *cons1, char *cons2, int gapped);
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40 int get_base_prime(char base);
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41 char *get_consensus(char *align[], char *quals[], int n_seqs, int seq_len, double thres,
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42 char qual_thres, int gapped);
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43 char *get_consensus_duplex(char *align1[], char *align2[], char *quals1[], char *quals2[],
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44 int n_seqs1, int n_seqs2, int seq_len, double cons_thres,
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45 char qual_thres, int gapped, char *method);
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46
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47
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48 // Tally the different bases at each position in an alignment.
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49 // Returns an array of arrays: for each position in the alignment, an array of the number of times
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50 // each base occurs at that position. The order of bases is as in the "BASES" constant.
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51 int **get_votes_simple(char *align[], int n_seqs, int seq_len) {
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52 int **votes = init_votes(seq_len);
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53
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54 // Tally votes for each base.
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55 int i, j;
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56 for (i = 0; i < n_seqs; i++) {
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57 for (j = 0; j < seq_len; j++) {
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58 // N.B.: Could write this without hardcoded literals, but it's about 40% slower.
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59 switch (toupper(align[i][j])) {
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60 case 'A':
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61 votes[j][0]++;
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62 break;
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63 case 'C':
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64 votes[j][1]++;
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65 break;
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66 case 'G':
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67 votes[j][2]++;
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68 break;
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69 case 'T':
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70 votes[j][3]++;
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71 break;
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72 case 'N':
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73 votes[j][4]++;
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74 break;
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75 case '-':
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76 votes[j][5]++;
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77 break;
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78 }
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79 }
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80 }
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81
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82 return votes;
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83 }
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84
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85
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86 // Tally votes for each base, ignoring bases with a quality score below "thres".
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87 int **get_votes_qual(char *align[], char *quals[], int n_seqs, int seq_len, char thres) {
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88 int **votes = init_votes(seq_len);
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89 int *window = malloc(sizeof(int) * WIN_LEN * 2);
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90 int win_edge;
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91
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92 // Tally votes for each base.
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93 char qual;
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94 int i, j;
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95 for (i = 0; i < n_seqs; i++) {
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96 win_edge = init_gap_qual_window(window, quals[i], seq_len);
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97 for (j = 0; j < seq_len; j++) {
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98 // Figure out the quality score of the base (or gap).
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99 if (align[i][j] == '-') {
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100 qual = get_gap_qual(window);
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101 } else {
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102 win_edge = push_qual(window, win_edge, quals[i], seq_len);
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103 qual = quals[i][j];
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104 }
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105 // Don't count bases whose quality is less than the threshold.
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106 if (qual < thres) {
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107 continue;
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108 }
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109 // N.B.: Could write this without hardcoded literals, but it's about 40% slower.
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110 switch (toupper(align[i][j])) {
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111 case 'A':
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112 votes[j][0]++;
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113 break;
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114 case 'C':
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115 votes[j][1]++;
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116 break;
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117 case 'G':
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118 votes[j][2]++;
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119 break;
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120 case 'T':
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121 votes[j][3]++;
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122 break;
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123 case 'N':
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124 votes[j][4]++;
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125 break;
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126 case '-':
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127 votes[j][5]++;
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128 break;
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129 }
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130 }
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131 }
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132
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133 free(window);
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134 return votes;
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135 }
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136
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137
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138 /* Tally votes for each base, weighting by the PHRED score of the base.
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139 * This is based on the theory of PHRED scores representing the literal probability of the base call
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140 * being erroneous. Thus, if two reads show a C at a position, both with PHRED 20 (1/100 chance of
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141 * error), then the chances of them both being wrong are 1/100 * 1/100 = 1/10000 (PHRED 40).
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142 * So, theoretically and intuitively, it makes sense to trust two PHRED 20 C's over one PHRED 30 A.
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143 * This seems better than arbitrarily deciding not to consider bases below a PHRED score threshold.
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144 * How to decide when not to call the base? We could just say that if no base's score total is above
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145 * a certain threshold, we call it an N. Theoretically, this threshold is the confidence we want in
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146 * our final base calls. This could even replace the arbitrary 3 reads for a consensus threshold.
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147 */
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148 int **get_votes_weighted(char *align[], char *quals[], int n_seqs, int seq_len) {
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149 int **votes = init_votes(seq_len);
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150 int *window = malloc(sizeof(int) * WIN_LEN * 2);
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151 int win_edge;
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152
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153 // Tally votes for each base.
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154 char qual;
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155 int i, j;
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156 for (i = 0; i < n_seqs; i++) {
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157 win_edge = init_gap_qual_window(window, quals[i], seq_len);
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158 for (j = 0; j < seq_len; j++) {
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159 // Figure out the quality score of the base (or gap).
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160 if (align[i][j] == '-') {
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161 qual = get_gap_qual(window);
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162 } else {
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163 win_edge = push_qual(window, win_edge, quals[i], seq_len);
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164 qual = quals[i][j];
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165 }
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166 // N.B.: Could write this without hardcoded literals, but it's about 40% slower.
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167 switch (toupper(align[i][j])) {
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168 case 'A':
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169 votes[j][0] += qual;
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170 break;
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171 case 'C':
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172 votes[j][1] += qual;
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173 break;
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174 case 'G':
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175 votes[j][2] += qual;
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176 break;
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177 case 'T':
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178 votes[j][3] += qual;
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179 break;
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180 case 'N':
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181 votes[j][4] += qual;
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182 break;
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183 case '-':
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184 votes[j][5] += qual;
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185 break;
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186 }
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187 }
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188 }
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189
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190 free(window);
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191 return votes;
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192 }
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193
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194
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195 /* Calculation of gap quality scores:
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196 * "window" is an array of length 2*WIN_LEN, holding the quality scores of the non-gap bases WIN_LEN
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197 * from the current one in both directions. When we're at the start or end, fill the slots beyond
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198 * the edge of the sequence with -1 as a sentinel for "N/A". For example, after the 2nd base in the
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199 * sequence, if WIN_LEN is 4 and there are no gaps yet, "window" should look something like this:
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200 * base coordinates 0 1 2 3 4 5
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201 * quality scores = 9 A > E B
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202 * array values [-1|-1|28|24||32|29|36|33]
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203 * Usage:
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204 * Allocate "window" and call init_gap_qual_window() to initialize it by filling its right side with
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205 * the first WIN_LEN non-gap quality scores in the sequence. It will also return "win_edge", which
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206 * tracks the coordinate of the rightmost quality score in "window".
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207 * Then, start traversing the array of quality scores. For each score, if it's a gap character, call
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208 * get_gap_qual() to get the computed quality score at the gap. Otherwise, call push_qual() to add
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209 * another quality score to the end of the window. This will keep the window filled with all non-gap
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210 * quality scores, and each time you call get_gap_qual(), you should be at the gap between the two
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211 * quality scores at the center of the window.
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212 */
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213
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214 // This does the initial fill of the window array, adding the first WIN_LEN bases to the right side
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215 // and filling the left side with -1's.
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216 int init_gap_qual_window(int *window, char *quals, int seq_len) {
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217 // Fill left side with -1's (no quality information).
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218 int i;
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219 for (i = 0; i < WIN_LEN; i++) {
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220 window[i] = -1;
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221 }
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222 // Fill right side with first WIN_LEN quality scores. Skip gaps, and if you run out of quality
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223 // scores (if seq_len < WIN_LEN), fill the rest with -1. Leave win_edge at the last base we added.
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224 i = WIN_LEN;
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225 int win_edge = -1;
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226 int quals_added = 0;
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227 while (quals_added < WIN_LEN) {
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228 win_edge++;
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229 if (win_edge >= seq_len) {
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230 win_edge = seq_len;
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231 window[i] = -1;
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232 i++;
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233 quals_added++;
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234 } else if (quals[win_edge] != GAP_CHAR) {
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235 window[i] = quals[win_edge];
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236 i++;
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237 quals_added++;
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238 }
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239 }
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240 return win_edge;
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241 }
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242
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243
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244 // Push the next non-gap quality score onto the right side of the window.
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245 int push_qual(int *window, int win_edge, char *quals, int seq_len) {
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246 // Find the next quality score that's not a gap.
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247 char next_qual = GAP_CHAR;
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248 while (next_qual == GAP_CHAR) {
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249 win_edge++;
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250 if (win_edge < seq_len) {
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251 next_qual = quals[win_edge];
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252 } else {
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253 win_edge = seq_len;
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254 next_qual = -1;
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255 }
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256 }
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257 // Shift all the quality scores left add the new one.
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258 int last_qual;
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259 int i;
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260 for (i = WIN_LEN*2 - 1; i >= 0; i--) {
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261 last_qual = window[i];
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262 window[i] = next_qual;
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263 next_qual = last_qual;
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264 }
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265 return win_edge;
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266 }
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267
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268
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269 // Compute the quality of the gap based on a weighted average of the quality scores in the window.
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270 // The scores near the center of the window are weighted higher than the ones further away.
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271 char get_gap_qual(int *window) {
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272 int score_sum = 0;
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273 int weight_sum = 0;
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274 int weight = 1;
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275 int i;
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276 for (i = 0; i < WIN_LEN*2; i++) {
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277 if (window[i] != -1) {
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278 score_sum += window[i] * weight;
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279 weight_sum += weight;
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280 }
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281 // Increase the weight until we get to the middle of the window (at WIN_LEN), then decrease it.
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282 if (i < WIN_LEN - 1) {
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283 weight++;
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284 } else if (i > WIN_LEN - 1) {
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285 weight--;
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286 }
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287 }
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288 if (weight_sum > 0) {
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289 // Divide by the sum of the weights to get the final quality score.
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290 return (char) (score_sum/weight_sum);
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291 } else {
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292 return '\0';
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293 }
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294 }
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295
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296
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297 void print_window(int *window, int win_edge) {
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298 printf("[");
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299 int i;
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300 for (i = 0; i < WIN_LEN*2; i++) {
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301 printf("%c", window[i]);
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302 if (i == WIN_LEN - 1) {
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303 printf("||");
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304 } else if (i == WIN_LEN*2 - 1) {
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305 printf("] %-2d\n", win_edge);
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306 } else {
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307 printf("|");
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308 }
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309 }
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310 }
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311
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312
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313 int **init_votes(int seq_len) {
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314 int **votes = malloc(sizeof(int *) * seq_len);
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315 int i, j;
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316 for (i = 0; i < seq_len; i++) {
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317 votes[i] = malloc(sizeof(int) * N_BASES);
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318 for (j = 0; j < N_BASES; j++) {
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319 votes[i][j] = 0;
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320 }
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321 }
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322 return votes;
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323 }
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324
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325
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326 void free_votes(int *votes[], int seq_len) {
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327 int i;
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328 for (i = 0; i < seq_len; i++) {
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329 free(votes[i]);
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330 }
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331 free(votes);
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332 }
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333
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334
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335 void print_votes(char *consensus, int *votes[], int seq_len) {
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336 int i, j;
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337 printf(" ");
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338 for (j = 0; j < N_BASES; j++) {
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339 printf(" %c ", BASES[j]);
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340 }
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341 printf("\n");
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342 for (i = 0; i < seq_len; i++) {
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343 printf("%c: ", consensus[i]);
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344 for (j = 0; j < N_BASES; j++) {
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345 if (votes[i][j]) {
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346 printf("%2d ", votes[i][j]);
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347 } else {
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348 printf(" ");
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349 }
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350 }
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351 printf("\n");
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352 }
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353 }
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354
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355
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356 // Take a consensus sequence which may have gaps ('-' characters) and remove them to produce the
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357 // actual final sequence. "cons_len" should be the length of the original, gapped, sequence.
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358 char *rm_gaps(char *consensus, int cons_len) {
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359 char *output = malloc(sizeof(char) * cons_len + 1);
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360 int i;
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361 int j = 0;
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362 for (i = 0; i < cons_len; i++) {
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363 if (consensus[i] != '-') {
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364 output[j] = consensus[i];
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365 j++;
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366 }
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367 }
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368 output[j] = '\0';
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369 return output;
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370 }
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371
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372
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373 char *build_consensus(int *votes[], int seq_len, double thres) {
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374 char *consensus = malloc(sizeof(char) * seq_len + 1);
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375
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376 int i, j;
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377 for (i = 0; i < seq_len; i++) {
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378 int total = 0;
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379 int max_vote = 0;
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380 char max_base = 'N';
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381 for (j = 0; j < N_BASES; j++) {
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382 total += votes[i][j];
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383 if (votes[i][j] > max_vote) {
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384 max_vote = votes[i][j];
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385 max_base = BASES[j];
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386 }
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387 if (total == 0) {
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388 consensus[i] = 'N';
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389 } else if ((double)max_vote/total > thres) {
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390 consensus[i] = max_base;
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391 } else {
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392 consensus[i] = 'N';
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393 }
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394 }
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395 }
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396
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397 consensus[seq_len] = '\0';
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398 return consensus;
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399 }
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400
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401
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402 // Build a consensus sequence from two alignments by weighting each equally and considering only
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403 // the frequency of each base in each alignment.
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404 char *build_consensus_duplex(int *votes1[], int *votes2[], int seq_len, double thres) {
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405 char *consensus = malloc(sizeof(char) * seq_len + 1);
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406
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407 int i, j;
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408 for (i = 0; i < seq_len; i++) {
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409 // Sum the total votes at this position.
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410 /*TODO: This does an extra loop through the votes to get the total so it can calculate actual
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411 * frequencies in the second pass. Technically, this information could be gathered when
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412 * originally tallying the votes in the get_votes functions. Or, the total could be assumed
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413 * to be n_seqs if every base always contributes a vote (even when it's not in "ACGTN-").
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414 */
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415 int total1 = 0;
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416 for (j = 0; j < N_BASES; j++) {
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417 total1 += votes1[i][j];
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418 }
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419 int total2 = 0;
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420 for (j = 0; j < N_BASES; j++) {
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421 total2 += votes2[i][j];
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422 }
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423 double max_freq = 0.0;
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424 char max_base = 'N';
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425 for (j = 0; j < N_BASES; j++) {
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426 // Get the frequency of each base.
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427 double freq1;
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428 if (total1 > 0) {
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429 freq1 = (double)votes1[i][j]/total1;
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430 }
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431 double freq2;
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432 if (total2 > 0) {
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433 freq2 = (double)votes2[i][j]/total2;
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434 }
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435 // frequency of the base = average of frequencies in the two sequences
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436 double avg_freq;
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437 if (total1 == 0 && total2 == 0) {
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438 avg_freq = -1.0;
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439 } else if (total1 == 0) {
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440 avg_freq = freq2;
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441 } else if (total2 == 0) {
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442 avg_freq = freq1;
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443 } else {
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444 avg_freq = (freq1 + freq2) / 2;
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445 }
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446 // Track the highest frequency seen.
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447 if (avg_freq > max_freq) {
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448 max_freq = avg_freq;
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449 max_base = BASES[j];
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450 }
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451 }
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452 if (max_freq > thres) {
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453 consensus[i] = max_base;
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454 } else {
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455 consensus[i] = 'N';
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456 }
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457 }
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458
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459 consensus[seq_len] = '\0';
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460 return consensus;
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461 }
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462
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463
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464 // "cons1" and "cons2" must be null-terminated strings of equal lengths.
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465 char *build_consensus_duplex_simple(char *cons1, char *cons2, int gapped) {
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466 int seq_len = strlen(cons1);
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467 char *cons = malloc(sizeof(char) * seq_len + 1);
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468 int i = 0;
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469 int base_prime1, base_prime2;
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470 while (cons1[i] != '\0' && cons2[i] != '\0') {
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471 base_prime1 = get_base_prime(cons1[i]);
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472 base_prime2 = get_base_prime(cons2[i]);
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473 cons[i] = IUPAC_BASES[base_prime1*base_prime2];
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474 i++;
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475 }
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476 cons[seq_len] = '\0';
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477 if (gapped) {
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478 return cons;
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479 } else {
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480 return rm_gaps(cons, seq_len);
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481 }
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482 }
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483
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484
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485 int get_base_prime(char base) {
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486 switch (base) {
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487 case 'A':
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488 return 2;
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489 case 'C':
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490 return 3;
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491 case 'G':
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492 return 5;
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493 case 'T':
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494 return 7;
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495 case 'N':
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496 return 11;
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497 case '-':
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498 return 13;
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499 default:
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500 return 0;
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501 }
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502 }
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503
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504
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505 // Convenience function to create a consensus in one step.
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506 // Give 0 as "quals" to not use quality scores, and -1.0 as "cons_thres" to use the default
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507 // consensus threshold when evaluating base votes.
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508 char *get_consensus(char *align[], char *quals[], int n_seqs, int seq_len, double cons_thres,
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509 char qual_thres, int gapped) {
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510 if (cons_thres == -1.0) {
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511 cons_thres = THRES_DEFAULT;
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512 }
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513 int **votes;
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514 if (quals == 0) {
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515 votes = get_votes_simple(align, n_seqs, seq_len);
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516 } else {
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517 votes = get_votes_qual(align, quals, n_seqs, seq_len, qual_thres);
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518 }
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519 char *consensus_gapped = build_consensus(votes, seq_len, cons_thres);
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520 char *consensus;
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521 if (gapped) {
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522 consensus = consensus_gapped;
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523 } else {
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524 consensus = rm_gaps(consensus_gapped, seq_len);
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525 }
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526 free_votes(votes, seq_len);
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527 return consensus;
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528 }
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529
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530
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531 char *get_consensus_duplex(char *align1[], char *align2[], char *quals1[], char *quals2[],
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532 int n_seqs1, int n_seqs2, int seq_len, double cons_thres,
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533 char qual_thres, int gapped, char *method) {
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534 if (cons_thres == -1.0) {
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535 cons_thres = THRES_DEFAULT;
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536 }
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537 int **votes1;
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538 int **votes2;
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539 if (quals1 == 0 || quals2 == 0) {
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540 votes1 = get_votes_simple(align1, n_seqs1, seq_len);
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541 votes2 = get_votes_simple(align2, n_seqs2, seq_len);
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542 } else {
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543 votes1 = get_votes_qual(align1, quals1, n_seqs1, seq_len, qual_thres);
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544 votes2 = get_votes_qual(align2, quals2, n_seqs2, seq_len, qual_thres);
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545 }
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546 char *consensus_gapped;
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547 if (!strncmp(method, "freq", 4)) {
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548 consensus_gapped = build_consensus_duplex(votes1, votes2, seq_len, cons_thres);
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549 } else if (!strncmp(method, "iupac", 5)) {
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550 char *cons1 = build_consensus(votes1, seq_len, cons_thres);
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551 char *cons2 = build_consensus(votes2, seq_len, cons_thres);
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552 consensus_gapped = build_consensus_duplex_simple(cons1, cons2, 1);
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553 } else {
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554 return "";
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555 }
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556 char *consensus;
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557 if (gapped) {
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558 consensus = consensus_gapped;
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559 } else {
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560 consensus = rm_gaps(consensus_gapped, seq_len);
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561 }
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562 free_votes(votes1, seq_len);
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563 free_votes(votes2, seq_len);
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564 return consensus;
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565 }
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566
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567
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568 void get_gap_quals(char *quals) {
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569 int seq_len = strlen(quals);
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570 int *window = malloc(sizeof(int) * WIN_LEN * 2);
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571 int win_edge = init_gap_qual_window(window, quals, seq_len);
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572 print_window(window, win_edge);
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573
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574 int i;
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575 char gap_qual;
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576 for (i = 0; i < seq_len; i++) {
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577 if (quals[i] == GAP_CHAR) {
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578 gap_qual = get_gap_qual(window);
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579 printf("gap %2d: %2d\n", i, gap_qual);
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580 } else {
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581 win_edge = push_qual(window, win_edge, quals, seq_len);
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582 print_window(window, win_edge);
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583 }
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584 }
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585 }
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586
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587
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588 int main(int argc, char *argv[]) {
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589 char **align = malloc(sizeof(char *) * (argc-1));
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590
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591 int seq_len = INT_MAX;
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592 int i;
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593 for (i = 1; i < argc; i++) {
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594 if (strlen(argv[i]) < seq_len) {
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595 seq_len = strlen(argv[i]);
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596 }
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597 align[i-1] = argv[i];
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598 }
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599
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600 if (argc <= 1) {
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601 return 1;
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602 }
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603
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604 get_gap_quals(align[0]);
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605 return 0;
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606
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607 int **votes = get_votes_simple(align, argc-1, seq_len);
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608 char *consensus = build_consensus(votes, seq_len, THRES_DEFAULT);
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609 print_votes(consensus, votes, seq_len);
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610 printf("%s\n", consensus);
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611 free_votes(votes, seq_len);
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612
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613 return 0;
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614 }