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1 /*****************************************************************************
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2 fastaFromBedMain.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 "fastaFromBed.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 "fastaFromBed"
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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
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36 // output files
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37 string fastaOutFile;
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38
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39 // checks for existence of parameters
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40 bool haveFastaDb = false;
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41 bool haveBed = false;
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42 bool haveFastaOut = false;
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43 bool useNameOnly = false;
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44 bool useFasta = true;
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45 bool useStrand = false;
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46
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47 // check to see if we should print out some help
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48 if(argc <= 1) showHelp = true;
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49
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50 for(int i = 1; i < argc; i++) {
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51 int parameterLength = (int)strlen(argv[i]);
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52
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53 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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54 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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55 showHelp = true;
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56 }
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57 }
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58
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59 if(showHelp) ShowHelp();
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60
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61 // do some parsing (all of these parameters require 2 strings)
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62 for(int i = 1; i < argc; i++) {
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63
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64 int parameterLength = (int)strlen(argv[i]);
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65
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66 if(PARAMETER_CHECK("-fi", 3, parameterLength)) {
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67 if ((i+1) < argc) {
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68 haveFastaDb = true;
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69 fastaDbFile = argv[i + 1];
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70 i++;
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71 }
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72 }
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73 else if(PARAMETER_CHECK("-fo", 3, parameterLength)) {
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74 if ((i+1) < argc) {
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75 haveFastaOut = true;
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76 fastaOutFile = argv[i + 1];
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77 i++;
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78 }
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79 }
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80 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
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81 if ((i+1) < argc) {
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82 haveBed = true;
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83 bedFile = argv[i + 1];
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84 i++;
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85 }
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86 }
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87 else if(PARAMETER_CHECK("-name", 5, parameterLength)) {
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88 useNameOnly = true;
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89 }
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90 else if(PARAMETER_CHECK("-tab", 4, parameterLength)) {
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91 useFasta = false;
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92 }
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93 else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
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94 useStrand = true;
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95 }
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96 else {
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97 cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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98 showHelp = true;
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99 }
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100 }
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101
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102 if (!haveFastaDb || !haveFastaOut || !haveBed) {
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103 showHelp = true;
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104 }
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105
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106 if (!showHelp) {
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107
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108 Bed2Fa *b2f = new Bed2Fa(useNameOnly, fastaDbFile, bedFile, fastaOutFile, useFasta, useStrand);
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109 delete b2f;
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110
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111 return 0;
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112 }
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113 else {
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114 ShowHelp();
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115 }
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116 }
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117
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118 void ShowHelp(void) {
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119
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120 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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121
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122 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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123
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124 cerr << "Summary: Extract DNA sequences into a fasta file based on feature coordinates." << endl << endl;
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125
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126 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> " << endl << endl;
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127
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128 cerr << "Options: " << endl;
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129 cerr << "\t-fi\tInput FASTA file" << endl;
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130 cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl;
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131 cerr << "\t-fo\tOutput file (can be FASTA or TAB-delimited)" << endl;
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132 cerr << "\t-name\tUse the name field for the FASTA header" << endl;
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133
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134 cerr << "\t-tab\tWrite output in TAB delimited format." << endl;
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135 cerr << "\t\t- Default is FASTA format." << endl << endl;
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136
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137 cerr << "\t-s\tForce strandedness. If the feature occupies the antisense strand," << endl;
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138 cerr << "\t\tthe sequence will be reverse complemented." << endl;
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139 cerr << "\t\t- By default, strand information is ignored." << endl << endl;
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140
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141
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142
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143 // end the program here
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144 exit(1);
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145
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146 }
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