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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 bedToIgv.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 "lineFileUtilities.h"
13 #include "bedFile.h"
14 #include "genomeFile.h"
15 #include "version.h"
16
17 #include <vector>
18 #include <iostream>
19 #include <fstream>
20 #include <stdlib.h>
21
22 using namespace std;
23
24 // define our program name
25 #define PROGRAM_NAME "bedToIgv"
26
27 // define our parameter checking macro
28 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
29
30 // function declarations
31 void ShowHelp(void);
32
33 void DetermineBedInput(BedFile *bed, string path, string sortType, string session,
34 bool collapse, bool useNames, string imageType, int slop);
35 void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session,
36 bool collapse, bool useNames, string imageType, int slop);
37
38
39 int main(int argc, char* argv[]) {
40
41 // our configuration variables
42 bool showHelp = false;
43
44 // input files
45 string bedFile = "stdin";
46 string imagePath = "./";
47 string sortType = "none";
48 string session = "none";
49 int slop = 0;
50 string imageType = "png";
51
52 bool haveBed = true;
53 bool collapse = false;
54 bool useNames = false;
55
56 for(int i = 1; i < argc; i++) {
57 int parameterLength = (int)strlen(argv[i]);
58
59 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
60 (PARAMETER_CHECK("--help", 5, parameterLength))) {
61 showHelp = true;
62 }
63 }
64
65 if(showHelp) ShowHelp();
66
67 // do some parsing (all of these parameters require 2 strings)
68 for(int i = 1; i < argc; i++) {
69
70 int parameterLength = (int)strlen(argv[i]);
71
72 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
73 if ((i+1) < argc) {
74 bedFile = argv[i + 1];
75 i++;
76 }
77 }
78 else if(PARAMETER_CHECK("-path", 5, parameterLength)) {
79 if ((i+1) < argc) {
80 imagePath = argv[i + 1];
81 i++;
82 }
83 }
84 else if(PARAMETER_CHECK("-sort", 5, parameterLength)) {
85 if ((i+1) < argc) {
86 sortType = argv[i + 1];
87 i++;
88 }
89 }
90 else if(PARAMETER_CHECK("-sess", 5, parameterLength)) {
91 if ((i+1) < argc) {
92 session = argv[i + 1];
93 i++;
94 }
95 }
96 else if(PARAMETER_CHECK("-clps", 5, parameterLength)) {
97 collapse = true;
98 }
99 else if(PARAMETER_CHECK("-name", 5, parameterLength)) {
100 useNames = true;
101 }
102 else if(PARAMETER_CHECK("-slop", 5, parameterLength)) {
103 if ((i+1) < argc) {
104 slop = atoi(argv[i + 1]);
105 i++;
106 }
107 }
108 else if(PARAMETER_CHECK("-img", 4, parameterLength)) {
109 if ((i+1) < argc) {
110 imageType = argv[i + 1];
111 i++;
112 }
113 }
114 else {
115 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
116 showHelp = true;
117 }
118 }
119
120 // make sure we have an input files
121 if (!haveBed ) {
122 cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl;
123 showHelp = true;
124 }
125 if (sortType != "none") {
126 if ((sortType != "base") && (sortType != "position") && (sortType != "strand") &&
127 (sortType != "quality") && (sortType != "sample") && (sortType != "readGroup")) {
128 cerr << endl << "*****" << endl << "*****ERROR: Invalid sort option. " << endl << "*****" << endl;
129 showHelp = true;
130 }
131 }
132 if (slop < 0) {
133 cerr << endl << "*****" << endl << "*****ERROR: Slop must be >= 0. " << endl << "*****" << endl;
134 showHelp = true;
135 }
136
137 if (!showHelp) {
138 BedFile *bed = new BedFile(bedFile);
139 DetermineBedInput(bed, imagePath, sortType, session, collapse, useNames, imageType, slop);
140 }
141 else {
142 ShowHelp();
143 }
144 }
145
146
147 void ShowHelp(void) {
148
149 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
150
151 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
152
153 cerr << "Summary: Creates a batch script to create IGV images " << endl;
154 cerr << " at each interval defined in a BED/GFF/VCF file." << endl << endl;
155
156 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl;
157
158 cerr << "Options: " << endl;
159
160 cerr << "\t-path\t" << "The full path to which the IGV snapshots should be written." << endl;
161 cerr << "\t\t(STRING) Default: ./" << endl << endl;
162
163 cerr << "\t-sess\t" << "The full path to an existing IGV session file to be " << endl;
164 cerr << "\t\tloaded prior to taking snapshots." << endl << endl;
165 cerr << "\t\t(STRING) Default is for no session to be loaded." << endl << endl;
166
167 cerr << "\t-sort\t" << "The type of BAM sorting you would like to apply to each image. " << endl;
168 cerr << "\t\tOptions: base, position, strand, quality, sample, and readGroup" << endl;
169 cerr << "\t\tDefault is to apply no sorting at all." << endl << endl;
170
171 cerr << "\t-clps\t" << "Collapse the aligned reads prior to taking a snapshot. " << endl;
172 cerr << "\t\tDefault is to no collapse." << endl << endl;
173
174 cerr << "\t-name\t" << "Use the \"name\" field (column 4) for each image's filename. " << endl;
175 cerr << "\t\tDefault is to use the \"chr:start-pos.ext\"." << endl << endl;
176
177 cerr << "\t-slop\t" << "Number of flanking base pairs on the left & right of the image." << endl;
178 cerr << "\t\t- (INT) Default = 0." << endl << endl;
179
180 cerr << "\t-img\t" << "The type of image to be created. " << endl;
181 cerr << "\t\tOptions: png, eps, svg" << endl;
182 cerr << "\t\tDefault is png." << endl << endl;
183
184 cerr << "Notes: " << endl;
185 cerr << "\t(1) The resulting script is meant to be run from within the IGV GUI version 1.5 or later." << endl;
186 cerr << "\t(2) Unless you use the -sess option, it is assumed that prior to running the script, " << endl;
187 cerr << "\t\tyou have loaded the proper genome, tracks and data files." << endl << endl;
188
189
190 // end the program here
191 exit(1);
192 }
193
194
195 void DetermineBedInput(BedFile *bed, string path, string sortType, string session,
196 bool collapse, bool useNames, string imageType, int slop) {
197
198 // dealing with a proper file
199 if (bed->bedFile != "stdin") {
200
201 ifstream bedStream(bed->bedFile.c_str(), ios::in);
202 if ( !bedStream ) {
203 cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl;
204 exit (1);
205 }
206 ProcessBed(bedStream, bed, path, sortType, session, collapse, useNames, imageType, slop);
207 }
208 // reading from stdin
209 else {
210 ProcessBed(cin, bed, path, sortType, session, collapse, useNames, imageType, slop);
211 }
212 }
213
214
215 void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session,
216 bool collapse, bool useNames, string imageType, int slop) {
217
218 // set the image path
219 cout << "snapshotDirectory " << path << endl;
220
221 // should we load a session
222 if (session != "none")
223 cout << "load " << session << endl;
224
225
226 BED bedEntry, nullBed;
227 int lineNum = 0;
228 BedLineStatus bedStatus;
229
230 bed->Open();
231 // process each BED entry and convert to an IGV request
232 while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
233 if (bedStatus == BED_VALID) {
234
235 string filename = bedEntry.chrom + "_" + ToString(bedEntry.start) + "_" + ToString(bedEntry.end);
236 string locus = bedEntry.chrom + ":" + ToString(bedEntry.start - slop) + "-" + ToString(bedEntry.end + slop);
237
238 if (useNames == true) {
239 if (bedEntry.name.empty() == false)
240 filename = filename + "_" + bedEntry.name;
241 else {
242 cerr << "Error: You requested that filenames be based upon the name field. However, it appears to be empty. Exiting!" << endl;
243 exit (1);
244 }
245 }
246 if (slop > 0) {
247 filename = filename + "_" + "slop" + ToString(slop);
248 }
249 // goto
250 cout << "goto " << locus << endl;
251
252 // sort
253 if (sortType != "none")
254 cout << "sort " << sortType << endl;
255
256 // collapse
257 if (collapse == true)
258 cout << "collapse" << endl;
259
260 // snapshot
261 cout << "snapshot " << filename << "." << imageType << endl;
262
263 // reset
264 bedEntry = nullBed;
265 }
266 }
267 // close up
268 bed->Close();
269 }