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1 //
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2 // sequenceUtils.cpp
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3 // BEDTools
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4 //
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5 // Created by Aaron Quinlan Spring 2009.
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6 // Copyright 2009 Aaron Quinlan. All rights reserved.
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7 //
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8 // Summary: Contains common functions for manipulating DNA sequences.
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9 //
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10 // Acknowledgment: I am grateful to Michael Stromberg for the code below to
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11 // reverse complement a sequence.
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12
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13 #include "sequenceUtils.h"
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14
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15 // Performs an in-place sequence reversal
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16 void reverseSequence(string &seq) {
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17 std::reverse(seq.begin(), seq.end());
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18 }
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19
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20 // Performs an in-place reverse complement conversion
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21 void reverseComplement(string &seq) {
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22
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23 // reverse the sequence
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24 reverseSequence(seq);
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25
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26 // swap the bases
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27 for(unsigned int i = 0; i < seq.length(); i++) {
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28 switch(seq[i]) {
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29 case 'A':
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30 seq[i] = 'T';
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31 break;
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32 case 'C':
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33 seq[i] = 'G';
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34 break;
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35 case 'G':
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36 seq[i] = 'C';
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37 break;
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38 case 'T':
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39 seq[i] = 'A';
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40 break;
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41 case 'a':
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42 seq[i] = 't';
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43 break;
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44 case 'c':
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45 seq[i] = 'g';
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46 break;
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47 case 'g':
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48 seq[i] = 'c';
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49 break;
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50 case 't':
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51 seq[i] = 'a';
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52 break;
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53 default:
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54 break;
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55 }
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56 }
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57 }
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58
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59
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60 void toLowerCase(std::string &seq)
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61 {
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62 const int length = seq.length();
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63 for(int i=0; i < length; ++i)
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64 {
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65 seq[i] = std::tolower(seq[i]);
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66 }
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67 }
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68
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69
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70 void toUpperCase(std::string &seq)
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71 {
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72 const int length = seq.length();
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73 for(int i=0; i < length; ++i)
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74 {
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75 seq[i] = std::toupper(seq[i]);
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76 }
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77 }
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78
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79
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80 void getDnaContent(const string &seq, int &a, int &c, int &g, int &t, int &n, int &other)
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81 {
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82 // swap the bases
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83 for(unsigned int i = 0; i < seq.length(); i++) {
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84 switch(seq[i]) {
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85 case 'A':
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86 case 'a':
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87 a++;
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88 break;
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89 case 'C':
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90 case 'c':
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91 c++;
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92 break;
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93 case 'G':
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94 case 'g':
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95 g++;
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96 break;
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97 case 'T':
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98 case 't':
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99 t++;
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100 break;
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101 case 'N':
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102 case 'n':
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103 n++;
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104 break;
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105 default:
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106 other++;
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107 break;
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108 }
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109 }
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110 }
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111
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112
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113 int countPattern(const string &seq, const string &pattern)
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114 {
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115 // swap the bases
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116 int patternLength = pattern.size();
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117 int patternCount = 0;
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118 for(unsigned int i = 0; i < seq.length(); i++) {
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119 if (seq.substr(i,patternLength) == pattern) {
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120 patternCount++;
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121 }
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122 }
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123 return patternCount;
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124 }
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125
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126
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