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
|
/*
* binsequencecommand.cpp
* Mothur
*
* Created by Sarah Westcott on 4/3/09.
* Copyright 2009 Schloss Lab UMASS Amhers. All rights reserved.
*
*/
#include "binsequencecommand.h"
//**********************************************************************************************************************
vector<string> BinSeqCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["count"] = tempOutNames;
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, "BinSeqCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string BinSeqCommand::getHelpString(){
try {
string helpString = "";
helpString += "The bin.seqs command parameters are list, fasta, name, count, label and group. The fasta and list are required, unless you have a valid current list and fasta file.\n";
helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
helpString += "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n";
helpString += "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n";
helpString += "The default value for label is all lines in your inputfile.\n";
helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "BinSeqCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string BinSeqCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],[distance],fasta"; } //makes file like: amazon.0.03.fasta
else if (type == "count") { pattern = "[filename],count_table"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "BinSeqCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(string option) : Command() {
try {
allLines = true;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
//check for required parameters
ValidParameters validParameter;
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not found") { //if there is a current phylip file, use it
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("You have no current fasta file and the fasta parameter is required.\n"); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
else { current->setFastaFile(fastafile); }
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not found") {
listfile = current->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter.\n"); }
else { m->mothurOut("You have no current list file and the list parameter is required.\n"); abort = true; }
}
else if (listfile == "not open") { listfile = ""; abort = true; }
else { current->setListFile(listfile); }
if (outputdir == "") { outputdir = util.hasPath(listfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
string namesfile = validParameter.validFile(parameters, "name");
if (namesfile == "not open") { namesfile = ""; abort = true; }
else if (namesfile == "not found") { namesfile = ""; }
else { current->setNameFile(namesfile); }
string groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); }
if ((namesfile != "") && (countfile != "")) { m->mothurOut("[ERROR]: you may only use one of the following: name or count.\n"); abort = true; }
if ((groupfile != "") && (countfile != "")) { m->mothurOut("[ERROR]: you may only use one of the following: group or count.\n"); abort=true; }
if (!abort) {
if ((namesfile != "") || (groupfile != "")) { //convert to count
string rootFileName = namesfile;
if (rootFileName == "") { rootFileName = groupfile; }
if (outputdir == "") { outputdir = util.hasPath(rootFileName); }
map<string, string> variables; variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(rootFileName));
string outputFileName = getOutputFileName("count", variables);
CountTable ct; ct.createTable(namesfile, groupfile, nullVector); ct.printCompressedTable(outputFileName);
outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
current->setCountFile(outputFileName);
countfile = outputFileName;
//list file will contain redund names since name file is provided - remove dups
string tempAccnos = namesfile + ".accnos.temp";
vector<string> namesOfSeqs = ct.getNamesOfSeqs();
util.printAccnos(tempAccnos, namesOfSeqs);
string inputString = "list=" + listfile + ", accnos=" + tempAccnos;
m->mothurOut("/******************************************/\n");
m->mothurOut("\nRunning command: get.seqs(" + inputString + ")\n");
current->setMothurCalling(true);
Command* getSeqsCommand = new GetSeqsCommand(inputString);
getSeqsCommand->execute();
string templistfile = getSeqsCommand->getOutputFiles()["list"][0];
string newName = util.getRootName(listfile) + "unique.list";
util.renameFile(templistfile, newName); listfile = newName;
namesfile = ""; groupfile = ""; util.mothurRemove(tempAccnos);
current->setListFile(listfile);
delete getSeqsCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
}
}
}
}
catch(exception& e) {
m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
exit(1);
}
}
//**********************************************************************************************************************
BinSeqCommand::~BinSeqCommand(){}
//**********************************************************************************************************************
int BinSeqCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
FastaMap fasta; fasta.readFastaFile(fastafile);
//if user gave a namesfile then use it
if (countfile != "") { ct.readTable(countfile, true, false); }
InputData input(listfile, "list", nullVector);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
int error = 0;
ListVector* list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
while (list != nullptr) {
if (m->getControl_pressed()) { delete list; break; }
error = process(list, fasta); delete list;
if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
}
if(m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
//set align file as new current fastafile
string currentFasta = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; current->setFastaFile(currentFasta); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "BinSeqCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
//return 1 if error, 0 otherwise
int BinSeqCommand::process(ListVector* list, FastaMap& fasta) {
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(listfile));
variables["[distance]"] = list->getLabel();
string outputFileName = getOutputFileName("fasta", variables);
ofstream out; util.openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
//for each bin in the list vector
vector<string> binLabels = list->getLabels();
for (int i = 0; i < list->size(); i++) {
if (m->getControl_pressed()) { return 1; }
string binnames = list->get(i);
vector<string> names;
util.splitAtComma(binnames, names);
for (int j = 0; j < names.size(); j++) {
string name = names[j];
//do work for that name
string sequence = fasta.getSequence(name);
if (countfile != "") {
if (sequence != "not found") {
if (ct.hasGroupInfo()) {
vector<string> groups = ct.getGroups(name);
string groupInfo = "";
for (int k = 0; k < groups.size()-1; k++) {
groupInfo += groups[k] + "-";
}
if (groups.size() != 0) { groupInfo += groups[groups.size()-1]; }
else { groupInfo = "not found"; }
name = name + "\t" + groupInfo + "\t" + binLabels[i] + "\tNumRep=" + toString(ct.getNumSeqs(name));
out << ">" << name << endl;
out << sequence << endl;
}else {
name = name + "\t" + binLabels[i] + "\tNumRep=" + toString(ct.getNumSeqs(name));
out << ">" << name << endl;
out << sequence << endl;
}
}else { m->mothurOut(name + " is missing from your fasta. Does your list file contain all sequence names or just the uniques?\n"); return 1; }
}else {
if (sequence != "not found") {
name = name + "\t" + binLabels[i];
out << ">" << name << endl;
out << sequence << endl;
}else { m->mothurOut(name + " is missing from your fasta or count file. Please correct. \n"); return 1; }
}
}
}
out.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "BinSeqCommand", "process");
exit(1);
}
}
//**********************************************************************************************************************
|
