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
|
/*
* getsabundcommand.cpp
* Mothur
*
* Created by Sarah Westcott on 6/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "getsabundcommand.h"
//**********************************************************************************************************************
vector<string> GetSAbundCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","sabund",false,false, true); parameters.push_back(plist);
CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false, false); parameters.push_back(pcount);
CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","sabund",false,false, true); parameters.push_back(prabund);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
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, "GetSAbundCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string GetSAbundCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.sabund command parameters is list, rabund, count and label. list or rabund is required unless a valid current file exists.\n";
helpString += "The count parameter allows you to provide a count file associated with your list file. If you clustered with a countfile the list file only contains the unique sequences and you will want to add the redundant counts into the sabund file, providing the count file allows you to do so.\n";
helpString += "The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n";
helpString += "The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n";
helpString += "Example get.sabund().\n";
helpString += "The default value for label is all labels in your inputfile.\n";
helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n";
helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string GetSAbundCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "sabund") { pattern = "[filename],sabund"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "GetRAbundCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["sabund"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(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 {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
map<string,string>::iterator it;
ValidParameters validParameter;
//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; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["sabund"] = tempOutNames;
//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("list");
//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["list"] = inputDir + it->second; }
}
it = parameters.find("rabund");
//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["rabund"] = inputDir + it->second; }
}
it = parameters.find("count");
//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["count"] = inputDir + it->second; }
}
}
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
if ((listfile == "") && (rabundfile == "")) {
//is there are current file available for any of these?
//give priority to shared, then list, then rabund, then sabund
//if there is a current shared file, use it
listfile = m->getListFile();
if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
else {
rabundfile = m->getRabundFile();
if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a list or rabund file."); m->mothurOutEndLine();
abort = true;
}
}
}
if ((countfile != "") && (listfile == "")) { m->mothurOut("[ERROR]: You can only use the count file with a list file, aborting.\n"); 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(inputfile); }
}
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetSAbundCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
filename = getOutputFileName("sabund", variables);
m->openOutputFile(filename, out);
if (countfile != "") {
processList(out);
}else {
InputData input(inputfile, format);
SAbundVector* sabund = input.getSAbundVector();
string lastLabel = sabund->getLabel();
//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;
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
}
if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
sabund = (input.getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
}
lastLabel = sabund->getLabel();
delete sabund;
sabund = (input.getSAbundVector());
}
//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) {
if (sabund != NULL) { delete sabund; }
sabund = (input.getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
delete sabund;
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
}
}
out.close();
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(filename); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
m->mothurOutEndLine();
//set sabund file as new current sabundfile
string current = "";
itTypes = outputTypes.find("sabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int GetSAbundCommand::processList(ofstream& out){
try {
CountTable ct;
ct.readTable(countfile, false, false);
InputData input(inputfile, format);
ListVector* list = input.getListVector();
string lastLabel = list->getLabel();
//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;
if (m->control_pressed) { delete list; return 0; }
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(list->getLabel()) == 1){
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(out);
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input.getListVector(lastLabel);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(out);
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
}
lastLabel = list->getLabel();
delete list;
list = input.getListVector();
}
//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) {
if (list != NULL) { delete list; }
list = input.getListVector(lastLabel);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(out);
delete rabund;
delete list;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "processList");
exit(1);
}
}
//**********************************************************************************************************************
int GetSAbundCommand::createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund){
try {
rabund->setLabel(list->getLabel());
for(int i = 0; i < list->getNumBins(); i++) {
if (m->control_pressed) { return 0; }
vector<string> binNames;
string bin = list->get(i);
m->splitAtComma(bin, binNames);
int total = 0;
for (int j = 0; j < binNames.size(); j++) {
total += ct.getNumSeqs(binNames[j]);
}
rabund->push_back(total);
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "createRabund");
exit(1);
}
}
//**********************************************************************************************************************
|
