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comparison BEDTools-Version-2.14.3/src/fastaFromBed/fastaFromBedMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 fastaFromBedMain.cpp
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "fastaFromBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "fastaFromBed"
19
20
21 // define our parameter checking macro
22 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
23
24 // function declarations
25 void ShowHelp(void);
26
27 int main(int argc, char* argv[]) {
28
29 // our configuration variables
30 bool showHelp = false;
31
32 // input files
33 string fastaDbFile;
34 string bedFile;
35
36 // output files
37 string fastaOutFile;
38
39 // checks for existence of parameters
40 bool haveFastaDb = false;
41 bool haveBed = false;
42 bool haveFastaOut = false;
43 bool useNameOnly = false;
44 bool useFasta = true;
45 bool useStrand = false;
46
47 // check to see if we should print out some help
48 if(argc <= 1) showHelp = true;
49
50 for(int i = 1; i < argc; i++) {
51 int parameterLength = (int)strlen(argv[i]);
52
53 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
54 (PARAMETER_CHECK("--help", 5, parameterLength))) {
55 showHelp = true;
56 }
57 }
58
59 if(showHelp) ShowHelp();
60
61 // do some parsing (all of these parameters require 2 strings)
62 for(int i = 1; i < argc; i++) {
63
64 int parameterLength = (int)strlen(argv[i]);
65
66 if(PARAMETER_CHECK("-fi", 3, parameterLength)) {
67 if ((i+1) < argc) {
68 haveFastaDb = true;
69 fastaDbFile = argv[i + 1];
70 i++;
71 }
72 }
73 else if(PARAMETER_CHECK("-fo", 3, parameterLength)) {
74 if ((i+1) < argc) {
75 haveFastaOut = true;
76 fastaOutFile = argv[i + 1];
77 i++;
78 }
79 }
80 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
81 if ((i+1) < argc) {
82 haveBed = true;
83 bedFile = argv[i + 1];
84 i++;
85 }
86 }
87 else if(PARAMETER_CHECK("-name", 5, parameterLength)) {
88 useNameOnly = true;
89 }
90 else if(PARAMETER_CHECK("-tab", 4, parameterLength)) {
91 useFasta = false;
92 }
93 else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
94 useStrand = true;
95 }
96 else {
97 cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
98 showHelp = true;
99 }
100 }
101
102 if (!haveFastaDb || !haveFastaOut || !haveBed) {
103 showHelp = true;
104 }
105
106 if (!showHelp) {
107
108 Bed2Fa *b2f = new Bed2Fa(useNameOnly, fastaDbFile, bedFile, fastaOutFile, useFasta, useStrand);
109 delete b2f;
110
111 return 0;
112 }
113 else {
114 ShowHelp();
115 }
116 }
117
118 void ShowHelp(void) {
119
120 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
121
122 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
123
124 cerr << "Summary: Extract DNA sequences into a fasta file based on feature coordinates." << endl << endl;
125
126 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> " << endl << endl;
127
128 cerr << "Options: " << endl;
129 cerr << "\t-fi\tInput FASTA file" << endl;
130 cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl;
131 cerr << "\t-fo\tOutput file (can be FASTA or TAB-delimited)" << endl;
132 cerr << "\t-name\tUse the name field for the FASTA header" << endl;
133
134 cerr << "\t-tab\tWrite output in TAB delimited format." << endl;
135 cerr << "\t\t- Default is FASTA format." << endl << endl;
136
137 cerr << "\t-s\tForce strandedness. If the feature occupies the antisense strand," << endl;
138 cerr << "\t\tthe sequence will be reverse complemented." << endl;
139 cerr << "\t\t- By default, strand information is ignored." << endl << endl;
140
141
142
143 // end the program here
144 exit(1);
145
146 }