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
|
//
// GetCoreMicroBiomeCommand.cpp
// Mothur
//
// Created by John Westcott on 5/8/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "getcoremicrobiomecommand.h"
//**********************************************************************************************************************
vector<string> GetCoreMicroBiomeCommand::setParameters(){
try {
CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(pshared);
CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(prelabund);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "","",false,false); parameters.push_back(poutput);
CommandParameter pabund("abundance", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pabund);
CommandParameter psamples("samples", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(psamples);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string GetCoreMicroBiomeCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.coremicrobiome determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.\n";
helpString += "The get.coremicrobiome parameters are: shared, relabund, groups, label, output, abundance and samples. Shared or relabund is required.\n";
helpString += "The label parameter is used to analyze specific labels in your input.\n";
helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
helpString += "The output parameter is used to specify whether you would like the fraction of OTU's or OTU count outputted. Options are fraction or count. Default=fraction.\n";
helpString += "The abundance parameter allows you to specify an abundance you would like the OTU names outputted for. Must be an integer between 0 and 100, indicating the relative abundance. \n";
helpString += "The samples parameter allows you to specify the minimum number of samples you would like the OTU names outputted for. Must be an interger between 1 and number of samples in your file.\n";
helpString += "The new command should be in the following format: get.coremicrobiome(shared=yourSharedFile)\n";
helpString += "get.coremicrobiom(shared=final.an.shared, abund=30)\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string GetCoreMicroBiomeCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "coremicrobiome") { pattern = "[filename],[tag],core.microbiome"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["coremicrobiome"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(string option) {
try {
abort = false; calledHelp = false; allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
//valid paramters for this command
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("relabund");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["relabund"] = inputDir + it->second; }
}
it = parameters.find("shared");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["shared"] = inputDir + it->second; }
}
}
vector<string> tempOutNames;
outputTypes["coremicrobiome"] = tempOutNames;
//check for parameters
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { inputFileName = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
relabundfile = validParameter.validFile(parameters, "relabund", true);
if (relabundfile == "not open") { abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
else { inputFileName = relabundfile; format = "relabund"; m->setRelAbundFile(relabundfile); }
if ((relabundfile == "") && (sharedfile == "")) {
//is there are current file available for either of these?
//give priority to shared, then relabund
sharedfile = m->getSharedFile();
if (sharedfile != "") { inputFileName = sharedfile; format="sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else {
relabundfile = m->getRelAbundFile();
if (relabundfile != "") { inputFileName = relabundfile; format="relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
abort = true;
}
}
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = m->hasPath(inputFileName); //if user entered a file with a path then preserve it
}
string groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else { m->splitAtDash(groups, Groups); }
m->setGroups(Groups);
string label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "fraction"; }
if ((output != "fraction") && (output != "count")) { m->mothurOut(output + " is not a valid output form. Options are fraction and count. I will use fraction."); m->mothurOutEndLine(); output = "fraction"; }
string temp = validParameter.validFile(parameters, "abundance", false); if (temp == "not found"){ temp = "-1"; }
m->mothurConvert(temp, abund);
if (abund != -1) {
if ((abund < 0) || (abund > 100)) { m->mothurOut(toString(abund) + " is not a valid number for abund. Must be an integer between 0 and 100.\n"); }
}
temp = validParameter.validFile(parameters, "samples", false); if (temp == "not found"){ temp = "-1"; }
m->mothurConvert(temp, samples);
}
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetCoreMicroBiomeCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
InputData input(inputFileName, format);
vector<SharedRAbundFloatVector*> lookup = input.getSharedRAbundFloatVectors();
string lastLabel = lookup[0]->getLabel();
if (samples != -1) {
if ((samples < 1) || (samples > lookup.size())) { m->mothurOut(toString(samples) + " is not a valid number for samples. Must be an integer between 1 and the number of samples in your file. Your file contains " + toString(lookup.size()) + " samples, so I will use that.\n"); samples = lookup.size(); }
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
createTable(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input.getSharedRAbundFloatVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
createTable(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
//restore real lastlabel to save below
lookup[0]->setLabel(saveLabel);
}
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//get next line to process
lookup = input.getSharedRAbundFloatVectors();
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input.getSharedRAbundFloatVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
createTable(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output files created by command
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
try {
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
variables["[tag]"] = lookup[0]->getLabel();
string outputFileName = getOutputFileName("coremicrobiome", variables);
outputNames.push_back(outputFileName); outputTypes["coremicrobiome"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
int numSamples = lookup.size();
int numOtus = lookup[0]->getNumBins();
//table is 100 by numsamples
//question we are answering is: what fraction of OTUs in a study have a relative abundance at or above %X
//in at least %Y samples. x goes from 0 to 100, y from 1 to numSamples
vector< vector<double> > table; table.resize(101);
for (int i = 0; i < table.size(); i++) { table[i].resize(numSamples, 0.0); }
map<int, vector<string> > otuNames;
if ((abund != -1) && (samples == -1)) { //fill with all samples
for (int i = 0; i < numSamples; i++) {
vector<string> temp;
otuNames[i+1] = temp;
}
}else if ((abund == -1) && (samples != -1)) { //fill with all relabund
for (int i = 0; i < 101; i++) {
vector<string> temp;
otuNames[i] = temp;
}
}else if ((abund != -1) && (samples != -1)) { //only one line is wanted
vector<string> temp;
otuNames[abund] = temp;
}
for (int i = 0; i < numOtus; i++) {
if (m->control_pressed) { break; }
//count number of samples in this otu with a relabund >= spot in count
vector<int> counts; counts.resize(101, 0);
for (int j = 0; j < lookup.size(); j++) {
double relabund = lookup[j]->getAbundance(i);
int wholeRelabund = (int) (floor(relabund*100));
for (int k = 0; k < wholeRelabund+1; k++) { counts[k]++; }
}
//add this otus info to table
for (int j = 0; j < table.size(); j++) {
for (int k = 0; k < counts[j]; k++) { table[j][k]++; }
if ((abund == -1) && (samples != -1)) { //we want all OTUs with this number of samples
if (counts[j] >= samples) { otuNames[j].push_back(m->currentSharedBinLabels[i]); }
}else if ((abund != -1) && (samples == -1)) { //we want all OTUs with this relabund
if (j == abund) {
for (int k = 0; k < counts[j]; k++) { otuNames[k+1].push_back(m->currentSharedBinLabels[i]); }
}
}else if ((abund != -1) && (samples != -1)) { //we want only OTUs with this relabund for this number of samples
if ((j == abund) && (counts[j] >= samples)) {
otuNames[j].push_back(m->currentSharedBinLabels[i]);
}
}
}
}
//format output
if (output == "fraction") { out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); }
out << "NumSamples\t";
//convert table counts to percents
for (int i = 0; i < table.size(); i++) {
out << "Relabund-" << i << "%\t";
if (m->control_pressed) { break; }
for (int j = 0; j < table[i].size(); j++) { if (output == "fraction") { table[i][j] /= (double) numOtus; } }
}
out << endl;
for (int i = 0; i < numSamples; i++) {
if (m->control_pressed) { break; }
out << i+1 << '\t';
for (int j = 0; j < table.size(); j++) { out << table[j][i] << '\t'; }
out << endl;
}
out.close();
if (m->control_pressed) { return 0; }
if ((samples != -1) || (abund != -1)) {
string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomelist";
outputNames.push_back(outputFileName2); outputTypes["coremicrobiome"].push_back(outputFileName2);
ofstream out2;
m->openOutputFile(outputFileName2, out2);
if ((abund == -1) && (samples != -1)) { //we want all OTUs with this number of samples
out2 << "Relabund%\tOTUList_for_samples=" << samples << "\n";
}else if ((abund != -1) && (samples == -1)) { //we want all OTUs with this relabund
out2 << "Samples\tOTUList_for_abund=" << abund << "\n";
}else if ((abund != -1) && (samples != -1)) { //we want only OTUs with this relabund for this number of samples
out2 << "Relabund%\tOTUList_for_samples=" << samples << "\n";
}
for (map<int, vector<string> >::iterator it = otuNames.begin(); it != otuNames.end(); it++) {
if (m->control_pressed) { break; }
vector<string> temp = it->second;
string list = m->makeList(temp);
out2 << it->first << '\t' << list << endl;
}
out2.close();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetCoreMicroBiomeCommand", "createTable");
exit(1);
}
}
//**********************************************************************************************************************
|
