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annotate seqtools.c @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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1 #include <stdlib.h>
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2 #include <string.h>
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3 #include <ctype.h>
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4 #include <math.h>
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5
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6 // ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz
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7 #define TRANS "TVGHEFCDIJMLKNOPQYWAABSXRZ[\\]^_`tvghefcdijmlknopqywaabsxrz"
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8 #define TRANS_OFFSET 65
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9 #define TRANS_LEN 57
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10
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11 char* get_revcomp(char *input);
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12 char get_char_comp(char c);
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13 int *get_diffs_simple(char *cons, char *seqs[], int n_seqs);
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14 double *get_diffs_frac_simple(char *cons, char *seqs[], int n_seqs);
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15 double **get_diffs_frac_binned(char *cons, char *seqs[], int n_seqs, int seq_len, int bins);
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16 char *transfer_gaps(char *gapped_seq, char *inseq, char gap_char1, char gap_char2);
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17 char **transfer_gaps_multi(int n_seqs, char *gapped_seqs[], char *inseqs[], char gap_char1, char gap_char2);
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20 // Return the reverse complement of a sequence.
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21 // Makes a new copy of the string, so the original is not modified.
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22 char* get_revcomp(char *input) {
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23 int length = strlen(input);
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24 char *output = malloc(sizeof(char) * length + 1);
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25 int i, j;
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26 for (i = 0, j = length - 1; i < length && j >= 0; i++, j--) {
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27 output[j] = get_char_comp(input[i]);
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28 }
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29 output[length] = '\0';
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30 return output;
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31 }
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32
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33
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34 // Return the complement of a base.
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35 // Uses a simple lookup table: a string with the complements of all possible sequence characters.
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36 char get_char_comp(char c) {
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37 int i = c - TRANS_OFFSET;
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38 if (i < 0 || i > TRANS_LEN) {
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39 return c;
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40 } else {
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41 return TRANS[i];
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42 }
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43 }
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45
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46 /* Take an existing alignment and consensus and compute the number of differences between each
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47 * sequence and the consensus.
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48 * Known bugs:
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49 * 1. Counts no differences in the following sequences:
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50 * consensus: GA---CA
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51 * seq 1: GA----A
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52 * seq 2: GA--ACA
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53 * 2. If a sequence starts with a gap, each base in the gap will be counted as a diff.
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54 */
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55 int *get_diffs_simple(char *cons, char *seqs[], int n_seqs) {
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56 int *diffs = malloc(sizeof(int) * n_seqs);
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57 int i = 0;
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58 // Uppercase the consensus.
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59 while (cons[i] != 0) {
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60 cons[i] = toupper(cons[i]);
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61 i++;
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62 }
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63 // Loop through the sequences in the alignment.
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64 for (i = 0; i < n_seqs; i++) {
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65 int in_gap;
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66 diffs[i] = 0;
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67 int j = 0;
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68 // Compare each base of the sequence to the consensus.
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69 while (seqs[i][j] != 0 && cons[j] != 0) {
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70 if (cons[j] != '-' && seqs[i][j] != '-') {
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71 in_gap = 0;
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72 }
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73 if (toupper(seqs[i][j]) != cons[j]) {
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74 if (!in_gap) {
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75 diffs[i]++;
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76 }
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77 }
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78 if (cons[j] == '-' || seqs[i][j] == '-') {
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79 in_gap = 1;
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80 }
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81 j++;
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82 }
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83 }
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84 return diffs;
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85 }
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86
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87
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88 // Convert the output of get_diffs_simple() from raw diff counts to fractions of the total sequence
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89 // lengths.
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90 //TODO: Don't count gaps in sequence length.
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91 double *get_diffs_frac_simple(char *cons, char *seqs[], int n_seqs) {
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92 int *diffs = get_diffs_simple(cons, seqs, n_seqs);
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93 double *fracs = malloc(sizeof(double) * n_seqs);
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94 int i;
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95 for (i = 0; i < n_seqs; i++) {
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96 int j = 0;
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97 while (seqs[i][j] != 0 && cons[j] != 0) {
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98 j++;
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99 }
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100 fracs[i] = (double)diffs[i]/j;
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101 }
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102 return fracs;
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103 }
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104
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105
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106 /* Take an existing alignment and consensus and compute the number of differences between each
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107 * sequence and the consensus. Break each sequence into bins and tally the differences in each bin.
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108 * Known bugs:
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109 * 1. counts no differences in the following sequences:
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110 * consensus: GA---CA
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111 * seq 1: GA----A
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112 * seq 2: GA--ACA
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113 * 2. If a bin starts with a gap, each base in the gap will be counted as a diff.
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114 */
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115 int **get_diffs_binned(char *cons, char *seqs[], int n_seqs, int seq_len, int bins) {
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116 int bin_size = (int)round((float)seq_len/bins);
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117 // Initialize the diffs 2d array.
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118 int **diffs = malloc(sizeof(int*) * n_seqs);
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119 int i, j;
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120 for (i = 0; i < n_seqs; i++) {
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121 diffs[i] = malloc(bins * sizeof(int));
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122 for (j = 0; j < bins; j++) {
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123 diffs[i][j] = 0;
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124 }
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125 }
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126 // Uppercase the consensus.
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127 while (cons[i] != 0) {
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128 cons[i] = toupper(cons[i]);
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129 i++;
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130 }
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131 int bin, in_gap;
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132 // Loop through the sequences in the alignment.
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133 for (i = 0; i < n_seqs; i++) {
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134 j = 0;
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135 // Compare each base of the sequence to the consensus.
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136 while (seqs[i][j] != 0 && cons[j] != 0) {
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137 bin = j/bin_size;
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138 if (bin >= bins) {
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139 break;
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140 }
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141 if (cons[j] != '-' && seqs[i][j] != '-') {
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142 in_gap = 0;
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143 }
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144 if (toupper(seqs[i][j]) != cons[j]) {
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145 if (!in_gap) {
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146 diffs[i][bin]++;
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147 }
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148 }
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149 if (cons[j] == '-' || seqs[i][j] == '-') {
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150 in_gap = 1;
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151 }
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152 j++;
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153 }
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154 }
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155 return diffs;
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156 }
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157
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158
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159 // Convert the output of get_diffs_binned() from raw diff counts to fractions of the total bin
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160 // lengths.
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161 //TODO: Don't count gaps in bin length.
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162 double **get_diffs_frac_binned(char *cons, char *seqs[], int n_seqs, int seq_len, int bins) {
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163 int bin_size = (int)round((float)seq_len/bins);
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164 int **diffs = get_diffs_binned(cons, seqs, n_seqs, seq_len, bins);
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165 double **fracs = malloc(sizeof(double*) * n_seqs);
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166 int i;
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167 for (i = 0; i < n_seqs; i++) {
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168 fracs[i] = malloc(sizeof(double) * bins);
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169 // Create and init array of lengths of the bins.
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170 int bin_lengths[bins];
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171 int bin;
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172 for (bin = 0; bin < bins; bin++) {
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173 bin_lengths[bin] = 0;
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174 }
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175 // Tally size of each bin.
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176 int j = 0;
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177 while (seqs[i][j] != 0 && cons[j] != 0) {
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178 int bin = j/bin_size;
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179 if (bin >= bins) {
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180 break;
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181 }
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182 bin_lengths[bin]++;
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183 j++;
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184 }
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185 // For each bin, calculate the diff fraction = diffs / bin_length.
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186 for (bin = 0; bin < bins; bin++) {
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187 fracs[i][bin] = (double)diffs[i][bin]/bin_lengths[bin];
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188 // printf("bin %d: %d / %d = %f\t", bin, diffs[i][bin], bin_lengths[bin], fracs[i][bin]);
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189 }
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190 // printf("\n");
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191 }
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192 return fracs;
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193 }
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194
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195
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196 // Take an input sequence and insert gaps according to another, already-aligned sequence with gaps.
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197 // Input strings must be null-terminated. "gap_char1" is the character used for gaps in
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198 // "gapped_seq", and "gap_char2" is the gap character in "inseq".
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199 // N.B.: The ungapped length of "gapped_seq" must be equal to the length of "inseq".
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200 char *transfer_gaps(char *gapped_seq, char *inseq, char gap_char1, char gap_char2) {
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201 if (gap_char1 == 0) {
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202 gap_char1 = '-';
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203 }
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204 if (gap_char2 == 0) {
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205 gap_char2 = '-';
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206 }
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207 int gapped_len = strlen(gapped_seq);
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208 char *outseq = malloc(sizeof(char) * gapped_len + 1);
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209
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210 // Transfer characters from inseq to outseq, except when gapped_seq has a gap at that spot
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211 // (insert a gap there instead).
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212 int g, o, i;
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213 for (g = 0, o = 0, i = 0; g < gapped_len; g++, o++) {
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214 if (gapped_seq[g] == gap_char1) {
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215 outseq[o] = gap_char2;
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216 } else {
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217 outseq[o] = inseq[i];
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218 i++;
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219 }
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220 }
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221 outseq[gapped_len] = '\0';
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222
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223 return outseq;
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224 }
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225
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226
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227 // Wrapper for transfer_gaps() when operating on a set of sequences at once.
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228 char **transfer_gaps_multi(int n_seqs, char *gapped_seqs[], char *inseqs[], char gap_char1,
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229 char gap_char2) {
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230 char **outseqs = malloc(sizeof(char *) * n_seqs);
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231 int i;
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232 for (i = 0; i < n_seqs; i++) {
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233 outseqs[i] = transfer_gaps(gapped_seqs[i], inseqs[i], gap_char1, gap_char2);
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234 }
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235 return outseqs;
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236 }