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1 /*****************************************************************************
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2 nucBedMain.cpp
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #include "nucBed.h"
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13 #include "version.h"
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14
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15 using namespace std;
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16
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17 // define our program name
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18 #define PROGRAM_NAME "nucBed"
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19
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20
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21 // define our parameter checking macro
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22 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
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23
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24 // function declarations
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25 void ShowHelp(void);
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26
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27 int main(int argc, char* argv[]) {
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28
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29 // our configuration variables
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30 bool showHelp = false;
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31
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32 // input files
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33 string fastaDbFile;
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34 string bedFile;
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35 string pattern;
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36
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37 // checks for existence of parameters
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38 bool haveFastaDb = false;
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39 bool haveBed = false;
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40 bool printSeq = false;
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41 bool hasPattern = false;
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42 bool forceStrand = false;
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43
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44 // check to see if we should print out some help
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45 if(argc <= 1) showHelp = true;
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46
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47 for(int i = 1; i < argc; i++) {
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48 int parameterLength = (int)strlen(argv[i]);
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49
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50 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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51 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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52 showHelp = true;
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53 }
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54 }
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55
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56 if(showHelp) ShowHelp();
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57
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58 // do some parsing (all of these parameters require 2 strings)
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59 for(int i = 1; i < argc; i++) {
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60
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61 int parameterLength = (int)strlen(argv[i]);
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62
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63 if(PARAMETER_CHECK("-fi", 3, parameterLength)) {
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64 if ((i+1) < argc) {
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65 haveFastaDb = true;
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66 fastaDbFile = argv[i + 1];
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67 i++;
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68 }
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69 }
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70 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
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71 if ((i+1) < argc) {
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72 haveBed = true;
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73 bedFile = argv[i + 1];
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74 i++;
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75 }
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76 }
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77 else if(PARAMETER_CHECK("-seq", 4, parameterLength)) {
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78 printSeq = true;
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79 }
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80 else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
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81 forceStrand = true;
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82 }
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83 else if(PARAMETER_CHECK("-pattern", 8, parameterLength)) {
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84 if ((i+1) < argc) {
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85 hasPattern = true;
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86 pattern = argv[i + 1];
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87 i++;
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88 }
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89 }
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90 else {
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91 cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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92 showHelp = true;
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93 }
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94 }
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95
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96 if (!haveFastaDb || !haveBed) {
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97 showHelp = true;
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98 }
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99
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100 if (!showHelp) {
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101
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102 NucBed *nuc = new NucBed(fastaDbFile, bedFile, printSeq, hasPattern, pattern, forceStrand);
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103 delete nuc;
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104
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105 return 0;
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106 }
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107 else {
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108 ShowHelp();
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109 }
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110 }
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111
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112 void ShowHelp(void) {
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113
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114 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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115
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116 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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117
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118 cerr << "Summary: Profiles the nucleotide content of intervals in a fasta file." << endl << endl;
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119
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120 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>" << endl << endl;
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121
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122 cerr << "Options: " << endl;
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123 cerr << "\t-fi\tInput FASTA file" << endl << endl;
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124 cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl << endl;
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125 cerr << "\t-s\tProfile the sequence according to strand." << endl << endl;
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126 cerr << "\t-seq\tPrint the extracted sequence" << endl << endl;
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127 cerr << "\t-pattern\tReport the number of times a user-defined sequence is observed (case-insensitive)." << endl << endl;
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128
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129
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130 cerr << "Output format: " << endl;
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131 cerr << "\tThe following information will be reported after each original BED entry:" << endl;
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132 cerr << "\t 1) %AT content" << endl;
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133 cerr << "\t 2) %GC content" << endl;
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134 cerr << "\t 3) Number of As observed" << endl;
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135 cerr << "\t 4) Number of Cs observed" << endl;
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136 cerr << "\t 5) Number of Gs observed" << endl;
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137 cerr << "\t 6) Number of Ts observed" << endl;
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138 cerr << "\t 7) Number of Ns observed" << endl;
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139 cerr << "\t 8) Number of other bases observed" << endl;
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140 cerr << "\t 9) The length of the explored sequence/interval." << endl;
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141 cerr << "\t 10) The sequence extracted from the FASTA file. (optional, if -seq is used)" << endl;
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142 cerr << "\t 11) The number of times a user defined pattern was observed. (optional, if -pattern is used.)" << endl;
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143
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144 // end the program here
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145 exit(1);
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146
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147 }
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