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","chimera-accnos",false,true,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,true); 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::getOutputPattern(string type) {
64 if (type == "chimera") { pattern = "[filename],bellerophon.chimeras"; }
65 else if (type == "accnos") { pattern = "[filename],bellerophon.accnos"; }
66 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
71 m->errorOut(e, "ChimeraBellerophonCommand", "getOutputPattern");
75 //**********************************************************************************************************************
76 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
78 abort = true; calledHelp = true;
80 vector<string> tempOutNames;
81 outputTypes["chimera"] = tempOutNames;
82 outputTypes["accnos"] = tempOutNames;
85 m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
89 //***************************************************************************************************************
90 ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) {
92 abort = false; calledHelp = false;
94 //allow user to run help
95 if(option == "help") { help(); abort = true; calledHelp = true; }
96 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
100 vector<string> myArray = setParameters();
102 OptionParser parser(option);
103 map<string,string> parameters = parser.getParameters();
105 ValidParameters validParameter("chimera.bellerophon");
106 map<string,string>::iterator it;
108 //check to make sure all parameters are valid for command
109 for (it = parameters.begin(); it != parameters.end(); it++) {
110 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
113 //initialize outputTypes
114 vector<string> tempOutNames;
115 outputTypes["chimera"] = tempOutNames;
116 outputTypes["accnos"] = tempOutNames;
118 //if the user changes the input directory command factory will send this info to us in the output parameter
119 string inputDir = validParameter.validFile(parameters, "inputdir", false);
120 if (inputDir == "not found"){ inputDir = ""; }
122 fastafile = validParameter.validFile(parameters, "fasta", false);
123 if (fastafile == "not found") {
124 //if there is a current fasta file, use it
125 string filename = m->getFastaFile();
126 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
127 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
129 m->splitAtDash(fastafile, fastaFileNames);
131 //go through files and make sure they are good, if not, then disregard them
132 for (int i = 0; i < fastaFileNames.size(); i++) {
135 if (fastaFileNames[i] == "current") {
136 fastaFileNames[i] = m->getFastaFile();
137 if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
139 m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
140 //erase from file list
141 fastaFileNames.erase(fastaFileNames.begin()+i);
148 if (inputDir != "") {
149 string path = m->hasPath(fastaFileNames[i]);
150 //if the user has not given a path then, add inputdir. else leave path alone.
151 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
157 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
159 //if you can't open it, try default location
160 if (ableToOpen == 1) {
161 if (m->getDefaultPath() != "") { //default path is set
162 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
163 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
165 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
167 fastaFileNames[i] = tryPath;
171 //if you can't open it, try default location
172 if (ableToOpen == 1) {
173 if (m->getOutputDir() != "") { //default path is set
174 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
175 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
177 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
179 fastaFileNames[i] = tryPath;
185 if (ableToOpen == 1) {
186 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
187 //erase from file list
188 fastaFileNames.erase(fastaFileNames.begin()+i);
191 m->setFastaFile(fastaFileNames[i]);
196 //make sure there is at least one valid file left
197 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
200 //if the user changes the output directory command factory will send this info to us in the output parameter
201 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
204 temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
205 filter = m->isTrue(temp);
207 temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
208 correction = m->isTrue(temp);
210 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
211 m->setProcessors(temp);
212 m->mothurConvert(temp, processors);
214 temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
215 m->mothurConvert(temp, window);
217 temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
218 m->mothurConvert(temp, increment);
221 catch(exception& e) {
222 m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
226 //***************************************************************************************************************
227 int ChimeraBellerophonCommand::execute(){
230 if (abort == true) { if (calledHelp) { return 0; } return 2; }
232 for (int i = 0; i < fastaFileNames.size(); i++) {
234 m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
236 int start = time(NULL);
238 chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);
240 if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
241 map<string, string> variables;
242 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
243 string outputFileName = getOutputFileName("chimera", variables);
244 string accnosFileName = getOutputFileName("accnos", variables);
246 chimera->getChimeras();
248 if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
252 MPI_File outMPIAccnos;
254 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
256 char outFilename[1024];
257 strcpy(outFilename, accnosFileName.c_str());
260 strcpy(FileName, outputFileName.c_str());
262 MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI); //comm, filename, mode, info, filepointer
263 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
265 numSeqs = chimera->print(outMPI, outMPIAccnos, "");
267 MPI_File_close(&outMPI);
268 MPI_File_close(&outMPIAccnos);
273 m->openOutputFile(outputFileName, out);
276 m->openOutputFile(accnosFileName, out2);
278 numSeqs = chimera->print(out, out2, "");
284 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; }
286 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
288 outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
289 outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
294 //set accnos file as new current accnosfile
296 itTypes = outputTypes.find("accnos");
297 if (itTypes != outputTypes.end()) {
298 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
301 m->mothurOutEndLine();
302 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
303 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
304 m->mothurOutEndLine();
309 catch(exception& e) {
310 m->errorOut(e, "ChimeraBellerophonCommand", "execute");
314 //**********************************************************************************************************************