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1 /*****************************************************************************
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2 shuffleBedMain.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 "shuffleBed.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 "shuffleBed"
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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 bedFile = "stdin";
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34 string excludeFile;
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35 string includeFile;
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36 string genomeFile;
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37
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38 bool haveBed = true;
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39 bool haveGenome = false;
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40 bool haveExclude = false;
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41 bool haveInclude = false;
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42 bool haveSeed = false;
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43 float overlapFraction = 0.0;
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44 int seed = -1;
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45 bool sameChrom = false;
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46
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47
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48 for(int i = 1; i < argc; i++) {
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49 int parameterLength = (int)strlen(argv[i]);
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50
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51 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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52 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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53 showHelp = true;
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54 }
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55 }
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56
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57 if(showHelp) ShowHelp();
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58
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59 // do some parsing (all of these parameters require 2 strings)
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60 for(int i = 1; i < argc; i++) {
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61
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62 int parameterLength = (int)strlen(argv[i]);
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63
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64 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
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65 if ((i+1) < argc) {
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66 bedFile = 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("-g", 2, parameterLength)) {
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71 if ((i+1) < argc) {
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72 haveGenome = true;
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73 genomeFile = 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("-excl", 5, parameterLength)) {
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78 if ((i+1) < argc) {
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79 haveExclude = true;
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80 excludeFile = argv[i + 1];
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81 i++;
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82 }
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83 }
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84 else if(PARAMETER_CHECK("-incl", 5, parameterLength)) {
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85 if ((i+1) < argc) {
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86 haveInclude = true;
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87 includeFile = argv[i + 1];
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88 i++;
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89 }
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90 }
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91 else if(PARAMETER_CHECK("-seed", 5, parameterLength)) {
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92 if ((i+1) < argc) {
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93 haveSeed = true;
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94 seed = atoi(argv[i + 1]);
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95 i++;
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96 }
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97 }
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98 else if(PARAMETER_CHECK("-chrom", 6, parameterLength)) {
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99 sameChrom = true;
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100 }
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101 else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
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102 if ((i+1) < argc) {
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103 overlapFraction = atof(argv[i + 1]);
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104 i++;
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105 }
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106 }
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107 else {
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108 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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109 showHelp = true;
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110 }
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111 }
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112
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113 // make sure we have both input files
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114 if (!haveBed || !haveGenome) {
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115 cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
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116 showHelp = true;
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117 }
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118
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119 if (haveInclude && haveExclude) {
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120 cerr << endl << "*****" << endl << "*****ERROR: Cannot use -incl and -excl together." << endl << "*****" << endl;
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121 showHelp = true;
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122 }
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123
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124 if (!showHelp) {
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125 BedShuffle *bc = new BedShuffle(bedFile, genomeFile, excludeFile, includeFile,
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126 haveSeed, haveExclude, haveInclude, sameChrom,
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127 overlapFraction, seed);
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128 delete bc;
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129 return 0;
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130 }
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131 else {
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132 ShowHelp();
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133 }
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134 }
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135
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136 void ShowHelp(void) {
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137
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138 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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139
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140 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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141
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142 cerr << "Summary: Randomly permute the locations of a feature file among a genome." << endl << endl;
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143
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144 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
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145
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146 cerr << "Options: " << endl;
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147 cerr << "\t-excl\t" << "A BED/GFF/VCF file of coordinates in which features in -i" << endl;
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148 cerr << "\t\tshould not be placed (e.g. gaps.bed)." << endl << endl;
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149
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150 cerr << "\t-incl\t" << "Instead of randomly placing features in a genome, the -incl" << endl;
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151 cerr << "\t\toptions defines a BED/GFF/VCF file of coordinates in which " << endl;
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152 cerr << "\t\tfeatures in -i should be randomly placed (e.g. genes.bed). " << endl << endl;
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153
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154 cerr << "\t-chrom\t" << "Keep features in -i on the same chromosome."<< endl;
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155 cerr << "\t\t- By default, the chrom and position are randomly chosen." << endl << endl;
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156
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157 cerr << "\t-seed\t" << "Supply an integer seed for the shuffling." << endl;
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158 cerr << "\t\t- By default, the seed is chosen automatically." << endl;
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159 cerr << "\t\t- (INTEGER)" << endl << endl;
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160
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161 cerr << "\t-f\t" << "Maximum overlap (as a fraction of the -i feature) with an -excl" << endl;
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162 cerr << "\t\tfeature that is tolerated before searching for a new, " << endl;
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163 cerr << "\t\trandomized locus. For example, -f 0.10 allows up to 10%" << endl;
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164 cerr << "\t\tof a randomized feature to overlap with a given feature" << endl;
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165 cerr << "\t\tin the -excl file. **Cannot be used with -incl file.**" << endl;
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166 cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
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167 cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
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168
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169 cerr << "Notes: " << endl;
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170 cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
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171 cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
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172 cerr << "\tFor example, Human (hg19):" << endl;
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173 cerr << "\tchr1\t249250621" << endl;
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174 cerr << "\tchr2\t243199373" << endl;
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175 cerr << "\t..." << endl;
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176 cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
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177
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178
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179 cerr << "Tips: " << endl;
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180 cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
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181 cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
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182 cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
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183 cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
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184
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185
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186 // end the program here
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187 exit(1);
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188 }
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