2 * chimerabellerophoncommand.cpp
5 * Created by westcott on 4/1/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "chimerabellerophoncommand.h"
11 #include "bellerophon.h"
13 //**********************************************************************************************************************
14 vector<string> ChimeraBellerophonCommand::setParameters(){
16 CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none",false,true); parameters.push_back(pfasta);
17 CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
18 CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
19 CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
20 CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
21 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
22 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
23 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
25 vector<string> myArray;
26 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
30 m->errorOut(e, "ChimeraBellerophonCommand", "setParameters");
34 //**********************************************************************************************************************
35 string ChimeraBellerophonCommand::getHelpString(){
37 string helpString = "";
38 helpString += "The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n";
39 helpString += "The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required, unless you have a valid current file.\n";
40 helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
41 helpString += "The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n";
42 helpString += "The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs, default=true.\n";
43 helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
45 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
47 helpString += "The window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n";
48 helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n";
49 helpString += "chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n";
50 helpString += "Example: chimera.bellerophon(fasta=AD.align, filter=True, correction=true, window=200) \n";
51 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
55 m->errorOut(e, "ChimeraBellerophonCommand", "getHelpString");
59 //**********************************************************************************************************************
60 string ChimeraBellerophonCommand::getOutputFileNameTag(string type, string inputName=""){
62 string outputFileName = "";
63 map<string, vector<string> >::iterator it;
65 //is this a type this command creates
66 it = outputTypes.find(type);
67 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
69 if (type == "chimera") { outputFileName = "bellerophon.chimeras"; }
70 else if (type == "accnos") { outputFileName = "bellerophon.accnos"; }
71 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
73 return outputFileName;
76 m->errorOut(e, "ChimeraBellerophonCommand", "getOutputFileNameTag");
80 //**********************************************************************************************************************
81 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
83 abort = true; calledHelp = true;
85 vector<string> tempOutNames;
86 outputTypes["chimera"] = tempOutNames;
87 outputTypes["accnos"] = tempOutNames;
90 m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
94 //***************************************************************************************************************
95 ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) {
97 abort = false; calledHelp = false;
99 //allow user to run help
100 if(option == "help") { help(); abort = true; calledHelp = true; }
101 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
105 vector<string> myArray = setParameters();
107 OptionParser parser(option);
108 map<string,string> parameters = parser.getParameters();
110 ValidParameters validParameter("chimera.bellerophon");
111 map<string,string>::iterator it;
113 //check to make sure all parameters are valid for command
114 for (it = parameters.begin(); it != parameters.end(); it++) {
115 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
118 //initialize outputTypes
119 vector<string> tempOutNames;
120 outputTypes["chimera"] = tempOutNames;
121 outputTypes["accnos"] = tempOutNames;
123 //if the user changes the input directory command factory will send this info to us in the output parameter
124 string inputDir = validParameter.validFile(parameters, "inputdir", false);
125 if (inputDir == "not found"){ inputDir = ""; }
127 fastafile = validParameter.validFile(parameters, "fasta", false);
128 if (fastafile == "not found") {
129 //if there is a current fasta file, use it
130 string filename = m->getFastaFile();
131 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
132 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
134 m->splitAtDash(fastafile, fastaFileNames);
136 //go through files and make sure they are good, if not, then disregard them
137 for (int i = 0; i < fastaFileNames.size(); i++) {
140 if (fastaFileNames[i] == "current") {
141 fastaFileNames[i] = m->getFastaFile();
142 if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
144 m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
145 //erase from file list
146 fastaFileNames.erase(fastaFileNames.begin()+i);
153 if (inputDir != "") {
154 string path = m->hasPath(fastaFileNames[i]);
155 //if the user has not given a path then, add inputdir. else leave path alone.
156 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
162 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
164 //if you can't open it, try default location
165 if (ableToOpen == 1) {
166 if (m->getDefaultPath() != "") { //default path is set
167 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
168 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
170 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
172 fastaFileNames[i] = tryPath;
176 //if you can't open it, try default location
177 if (ableToOpen == 1) {
178 if (m->getOutputDir() != "") { //default path is set
179 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
180 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
182 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
184 fastaFileNames[i] = tryPath;
190 if (ableToOpen == 1) {
191 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
192 //erase from file list
193 fastaFileNames.erase(fastaFileNames.begin()+i);
196 m->setFastaFile(fastaFileNames[i]);
201 //make sure there is at least one valid file left
202 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
205 //if the user changes the output directory command factory will send this info to us in the output parameter
206 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
209 temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
210 filter = m->isTrue(temp);
212 temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
213 correction = m->isTrue(temp);
215 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
216 m->setProcessors(temp);
217 m->mothurConvert(temp, processors);
219 temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
220 m->mothurConvert(temp, window);
222 temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
223 m->mothurConvert(temp, increment);
226 catch(exception& e) {
227 m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
231 //***************************************************************************************************************
232 int ChimeraBellerophonCommand::execute(){
235 if (abort == true) { if (calledHelp) { return 0; } return 2; }
237 for (int i = 0; i < fastaFileNames.size(); i++) {
239 m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
241 int start = time(NULL);
243 chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);
245 if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
246 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
247 string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("accnos");
249 chimera->getChimeras();
251 if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
255 MPI_File outMPIAccnos;
257 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
259 char outFilename[1024];
260 strcpy(outFilename, accnosFileName.c_str());
263 strcpy(FileName, outputFileName.c_str());
265 MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI); //comm, filename, mode, info, filepointer
266 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
268 numSeqs = chimera->print(outMPI, outMPIAccnos, "");
270 MPI_File_close(&outMPI);
271 MPI_File_close(&outMPIAccnos);
276 m->openOutputFile(outputFileName, out);
279 m->openOutputFile(accnosFileName, out2);
281 numSeqs = chimera->print(out, out2, "");
287 if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(outputFileName); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); delete chimera; return 0; }
289 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
291 outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
292 outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
297 //set accnos file as new current accnosfile
299 itTypes = outputTypes.find("accnos");
300 if (itTypes != outputTypes.end()) {
301 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
304 m->mothurOutEndLine();
305 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
306 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
307 m->mothurOutEndLine();
312 catch(exception& e) {
313 m->errorOut(e, "ChimeraBellerophonCommand", "execute");
317 //**********************************************************************************************************************