forked from mothur/mothur
-
Notifications
You must be signed in to change notification settings - Fork 1
/
chimeracheckrdp.cpp
489 lines (362 loc) · 15.5 KB
/
chimeracheckrdp.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
/*
* chimeracheckrdp.cpp
* Mothur
*
* Created by westcott on 9/8/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "chimeracheckrdp.h"
//***************************************************************************************************************
ChimeraCheckRDP::ChimeraCheckRDP(string filename, string temp, string n, bool s, int inc, int k, string o) : Chimera() {
try {
fastafile = filename;
templateFileName = temp;
name = n;
svg = s;
increment = inc;
kmerSize = k;
outputDir = o;
templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand());
m->mothurOutEndLine();
kmer = new Kmer(kmerSize);
if (name != "") {
readName(name); //fills name map with names of seqs the user wants to have .svg for.
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "ChimeraCheckRDP");
exit(1);
}
}
//***************************************************************************************************************
ChimeraCheckRDP::~ChimeraCheckRDP() {
try {
delete templateDB;
delete kmer;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "~ChimeraCheckRDP");
exit(1);
}
}
//***************************************************************************************************************
Sequence ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
try {
m->mothurOut("Processing: " + querySeq->getName()); m->mothurOutEndLine();
out << querySeq->getName() << endl;
out << "IS scores: " << '\t';
for (int k = 0; k < IS.size(); k++) {
out << IS[k].score << '\t';
}
out << endl;
if (svg) {
if (name != "") { //if user has specific names
map<string, string>::iterator it = names.find(querySeq->getName());
if (it != names.end()) { //user wants pic of this
makeSVGpic(IS); //zeros out negative results
}
}else{//output them all
makeSVGpic(IS); //zeros out negative results
}
}
return *querySeq;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "print");
exit(1);
}
}
#ifdef USE_MPI
//***************************************************************************************************************
Sequence ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
try {
cout << "Processing: " << querySeq->getName() << endl;
string outString = "";
outString += querySeq->getName() + "\nIS scores: \t";
for (int k = 0; k < IS.size(); k++) {
outString += toString(IS[k].score) + "\t";
}
outString += "\n";
MPI_Status status;
int length = outString.length();
char* buf = new char[length];
memcpy(buf, outString.c_str(), length);
MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
delete buf;
if (svg) {
if (name != "") { //if user has specific names
map<string, string>::iterator it = names.find(querySeq->getName());
if (it != names.end()) { //user wants pic of this
makeSVGpic(IS); //zeros out negative results
}
}else{//output them all
makeSVGpic(IS); //zeros out negative results
}
}
return *querySeq;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "print");
exit(1);
}
}
#endif
//***************************************************************************************************************
int ChimeraCheckRDP::getChimeras(Sequence* query) {
try {
IS.clear();
querySeq = query;
closest = templateDB->findClosestSequence(query);
IS = findIS();
//determine chimera report cutoff - window score above 95%
//getCutoff(); - not very acurate predictor
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "getChimeras");
exit(1);
}
}
//***************************************************************************************************************
vector<sim> ChimeraCheckRDP::findIS() {
try {
vector< map<int, int> > queryKmerInfo; //vector of maps - each entry in the vector is a map of the kmers up to that spot in the unaligned seq
//example: seqKmerInfo[50] = map containing the kmers found in the first 50 + kmersize characters of ecoli.
//i chose to store the kmers numbers in a map so you wouldn't have to check for dupilcate entries and could easily find the
//kmers 2 seqs had in common. There may be a better way to do this thats why I am leaving so many comments...
vector< map<int, int> > subjectKmerInfo;
vector<sim> isValues;
string queryName = querySeq->getName();
string seq = querySeq->getUnaligned();
queryKmerInfo = kmer->getKmerCounts(seq);
subjectKmerInfo = kmer->getKmerCounts(closest.getUnaligned());
//find total kmers you have in common with closest[query] by looking at the last entry in the vector of maps for each
int nTotal = calcKmers(queryKmerInfo[(queryKmerInfo.size()-1)], subjectKmerInfo[(subjectKmerInfo.size()-1)]);
//you don't want the starting point to be virtually at hte end so move it in 10%
int start = seq.length() / 10;
//for each window
for (int f = start; f < (seq.length() - start); f+=increment) {
if (m->control_pressed) { return isValues; }
if ((f - kmerSize) < 0) { m->mothurOut("Your sequence is too short for your kmerSize."); m->mothurOutEndLine(); exit(1); }
sim temp;
string fragLeft = seq.substr(0, f); //left side of breakpoint
string fragRight = seq.substr(f); //right side of breakpoint
//make a sequence of the left side and right side
Sequence* left = new Sequence(queryName, fragLeft);
Sequence* right = new Sequence(queryName, fragRight);
//find seqs closest to each fragment
Sequence closestLeft = templateDB->findClosestSequence(left);
Sequence closestRight = templateDB->findClosestSequence(right);
//get kmerinfo for the closest left
vector< map<int, int> > closeLeftKmerInfo = kmer->getKmerCounts(closestLeft.getUnaligned());
//get kmerinfo for the closest right
vector< map<int, int> > closeRightKmerInfo = kmer->getKmerCounts(closestRight.getUnaligned());
//right side is tricky - since the counts grow on eachother to find the correct counts of only the right side you must subtract the counts of the left side
//iterate through left sides map to subtract the number of times you saw things before you got the the right side
map<int, int> rightside = queryKmerInfo[queryKmerInfo.size()-1];
for (map<int, int>::iterator itleft = queryKmerInfo[f-kmerSize].begin(); itleft != queryKmerInfo[f-kmerSize].end(); itleft++) {
int howManyTotal = queryKmerInfo[queryKmerInfo.size()-1][itleft->first]; //times that kmer was seen in total
//itleft->second is times it was seen in left side, so howmanytotal - leftside should give you right side
int howmanyright = howManyTotal - itleft->second;
//if any were seen just on the left erase
if (howmanyright == 0) {
rightside.erase(itleft->first);
}
}
map<int, int> closerightside = closeRightKmerInfo[closeRightKmerInfo.size()-1];
for (map<int, int>::iterator itright = closeRightKmerInfo[f-kmerSize].begin(); itright != closeRightKmerInfo[f-kmerSize].end(); itright++) {
int howManyTotal = closeRightKmerInfo[(closeRightKmerInfo.size()-1)][itright->first]; //times that kmer was seen in total
//itleft->second is times it was seen in left side, so howmanytotal - leftside should give you right side
int howmanyright = howManyTotal - itright->second;
//if any were seen just on the left erase
if (howmanyright == 0) {
closerightside.erase(itright->first);
}
}
int nLeft = calcKmers(closeLeftKmerInfo[f-kmerSize], queryKmerInfo[f-kmerSize]);
int nRight = calcKmers(closerightside, rightside);
int is = nLeft + nRight - nTotal;
//save IS, leftparent, rightparent, breakpoint
temp.leftParent = closestLeft.getName();
temp.rightParent = closestRight.getName();
temp.score = is;
temp.midpoint = f;
isValues.push_back(temp);
delete left;
delete right;
}
return isValues;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "findIS");
exit(1);
}
}
//***************************************************************************************************************
void ChimeraCheckRDP::readName(string namefile) {
try{
string name;
#ifdef USE_MPI
MPI_File inMPI;
MPI_Offset size;
MPI_Status status;
//char* inFileName = new char[namefile.length()];
//memcpy(inFileName, namefile.c_str(), namefile.length());
char inFileName[1024];
strcpy(inFileName, namefile.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
MPI_File_get_size(inMPI, &size);
//delete inFileName;
char* buffer = new char[size];
MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
string tempBuf = buffer;
if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
istringstream iss (tempBuf,istringstream::in);
delete buffer;
while(!iss.eof()) {
iss >> name; m->gobble(iss);
names[name] = name;
}
MPI_File_close(&inMPI);
#else
ifstream in;
m->openInputFile(namefile, in);
while (!in.eof()) {
in >> name; m->gobble(in);
names[name] = name;
}
in.close();
#endif
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "readName");
exit(1);
}
}
//***************************************************************************************************************
//find the smaller map and iterate through it and count kmers in common
int ChimeraCheckRDP::calcKmers(map<int, int> query, map<int, int> subject) {
try{
int common = 0;
map<int, int>::iterator smallone;
map<int, int>::iterator largeone;
if (query.size() < subject.size()) {
for (smallone = query.begin(); smallone != query.end(); smallone++) {
largeone = subject.find(smallone->first);
//if you found it they have that kmer in common
if (largeone != subject.end()) { common++; }
}
}else {
for (smallone = subject.begin(); smallone != subject.end(); smallone++) {
largeone = query.find(smallone->first);
//if you found it they have that kmer in common
if (largeone != query.end()) { common++; }
}
}
return common;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "calcKmers");
exit(1);
}
}
#ifdef USE_MPI
//***************************************************************************************************************
void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
try{
string file = outputDir + querySeq->getName() + ".chimeracheck.svg";
MPI_File outSVG;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
//char* FileName = new char[file.length()];
//memcpy(FileName, file.c_str(), file.length());
char FileName[1024];
strcpy(FileName, file.c_str());
MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outSVG); //comm, filename, mode, info, filepointer
//delete FileName;
int width = (info.size()*5) + 150;
string outString = "";
outString += "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 " + toString(width) + "\">\n";
outString += "<g>\n";
outString += "<text fill=\"black\" class=\"seri\" x=\"" + toString((width / 2) - 150) + "\" y=\"25\">Plotted IS values for " + querySeq->getName() + "</text>\n";
outString += "<line x1=\"75\" y1=\"600\" x2=\"" + toString((info.size()*5) + 75) + "\" y2=\"600\" stroke=\"black\" stroke-width=\"2\"/>\n";
outString += "<line x1=\"75\" y1=\"600\" x2=\"75\" y2=\"125\" stroke=\"black\" stroke-width=\"2\"/>\n";
outString += "<text fill=\"black\" class=\"seri\" x=\"80\" y=\"620\">" + toString(info[0].midpoint) + "</text>\n";
outString += "<text fill=\"black\" class=\"seri\" x=\"" + toString((info.size()*5) + 75) + "\" y=\"620\">" + toString(info[info.size()-1].midpoint) + "</text>\n";
outString += "<text fill=\"black\" class=\"seri\" x=\"" + toString((width / 2) - 150) + "\" y=\"650\">Base Positions</text>\n";
outString += "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"580\">0</text>\n";
outString += "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"350\">IS</text>\n";
//find max is score
float biggest = 0.0;
for (int i = 0; i < info.size(); i++) {
if (info[i].score > biggest) {
biggest = info[i].score;
}
}
outString += "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"135\">" + toString(biggest) + "</text>\n";
int scaler2 = 500 / biggest;
outString += "<polyline fill=\"none\" stroke=\"red\" stroke-width=\"2\" points=\"";
//160,200 180,230 200,210 234,220\"/> ";
for (int i = 0; i < info.size(); i++) {
if(info[i].score < 0) { info[i].score = 0; }
outString += toString(((i*5) + 75)) + "," + toString((600 - (info[i].score * scaler2))) + " ";
}
outString += "\"/> ";
outString += "</g>\n</svg>\n";
MPI_Status status;
int length = outString.length();
char* buf2 = new char[length];
memcpy(buf2, outString.c_str(), length);
MPI_File_write(outSVG, buf2, length, MPI_CHAR, &status);
delete buf2;
MPI_File_close(&outSVG);
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "makeSVGpic");
exit(1);
}
}
#else
//***************************************************************************************************************
void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
try{
string file = outputDir + querySeq->getName() + ".chimeracheck.svg";
ofstream outsvg;
m->openOutputFile(file, outsvg);
int width = (info.size()*5) + 150;
outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 " + toString(width) + "\">\n";
outsvg << "<g>\n";
outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((width / 2) - 150) + "\" y=\"25\">Plotted IS values for " + querySeq->getName() + "</text>\n";
outsvg << "<line x1=\"75\" y1=\"600\" x2=\"" + toString((info.size()*5) + 75) + "\" y2=\"600\" stroke=\"black\" stroke-width=\"2\"/>\n";
outsvg << "<line x1=\"75\" y1=\"600\" x2=\"75\" y2=\"125\" stroke=\"black\" stroke-width=\"2\"/>\n";
outsvg << "<text fill=\"black\" class=\"seri\" x=\"80\" y=\"620\">" + toString(info[0].midpoint) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((info.size()*5) + 75) + "\" y=\"620\">" + toString(info[info.size()-1].midpoint) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((width / 2) - 150) + "\" y=\"650\">Base Positions</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"580\">0</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"350\">IS</text>\n";
//find max is score
float biggest = 0.0;
for (int i = 0; i < info.size(); i++) {
if (info[i].score > biggest) {
biggest = info[i].score;
}
}
outsvg << "<text fill=\"black\" class=\"seri\" x=\"50\" y=\"135\">" + toString(biggest) + "</text>\n";
int scaler2 = 500 / biggest;
outsvg << "<polyline fill=\"none\" stroke=\"red\" stroke-width=\"2\" points=\"";
//160,200 180,230 200,210 234,220\"/> ";
for (int i = 0; i < info.size(); i++) {
if(info[i].score < 0) { info[i].score = 0; }
outsvg << ((i*5) + 75) << "," << (600 - (info[i].score * scaler2)) << " ";
}
outsvg << "\"/> ";
outsvg << "</g>\n</svg>\n";
outsvg.close();
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckRDP", "makeSVGpic");
exit(1);
}
}
#endif
//***************************************************************************************************************/