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comparison BEDTools-Version-2.14.3/src/utils/sequenceUtilities/sequenceUtils.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 //
2 // sequenceUtils.cpp
3 // BEDTools
4 //
5 // Created by Aaron Quinlan Spring 2009.
6 // Copyright 2009 Aaron Quinlan. All rights reserved.
7 //
8 // Summary: Contains common functions for manipulating DNA sequences.
9 //
10 // Acknowledgment: I am grateful to Michael Stromberg for the code below to
11 // reverse complement a sequence.
12
13 #include "sequenceUtils.h"
14
15 // Performs an in-place sequence reversal
16 void reverseSequence(string &seq) {
17 std::reverse(seq.begin(), seq.end());
18 }
19
20 // Performs an in-place reverse complement conversion
21 void reverseComplement(string &seq) {
22
23 // reverse the sequence
24 reverseSequence(seq);
25
26 // swap the bases
27 for(unsigned int i = 0; i < seq.length(); i++) {
28 switch(seq[i]) {
29 case 'A':
30 seq[i] = 'T';
31 break;
32 case 'C':
33 seq[i] = 'G';
34 break;
35 case 'G':
36 seq[i] = 'C';
37 break;
38 case 'T':
39 seq[i] = 'A';
40 break;
41 case 'a':
42 seq[i] = 't';
43 break;
44 case 'c':
45 seq[i] = 'g';
46 break;
47 case 'g':
48 seq[i] = 'c';
49 break;
50 case 't':
51 seq[i] = 'a';
52 break;
53 default:
54 break;
55 }
56 }
57 }
58
59
60 void toLowerCase(std::string &seq)
61 {
62 const int length = seq.length();
63 for(int i=0; i < length; ++i)
64 {
65 seq[i] = std::tolower(seq[i]);
66 }
67 }
68
69
70 void toUpperCase(std::string &seq)
71 {
72 const int length = seq.length();
73 for(int i=0; i < length; ++i)
74 {
75 seq[i] = std::toupper(seq[i]);
76 }
77 }
78
79
80 void getDnaContent(const string &seq, int &a, int &c, int &g, int &t, int &n, int &other)
81 {
82 // swap the bases
83 for(unsigned int i = 0; i < seq.length(); i++) {
84 switch(seq[i]) {
85 case 'A':
86 case 'a':
87 a++;
88 break;
89 case 'C':
90 case 'c':
91 c++;
92 break;
93 case 'G':
94 case 'g':
95 g++;
96 break;
97 case 'T':
98 case 't':
99 t++;
100 break;
101 case 'N':
102 case 'n':
103 n++;
104 break;
105 default:
106 other++;
107 break;
108 }
109 }
110 }
111
112
113 int countPattern(const string &seq, const string &pattern)
114 {
115 // swap the bases
116 int patternLength = pattern.size();
117 int patternCount = 0;
118 for(unsigned int i = 0; i < seq.length(); i++) {
119 if (seq.substr(i,patternLength) == pattern) {
120 patternCount++;
121 }
122 }
123 return patternCount;
124 }
125
126