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 //***************************************************************************************************************
15 ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) {
19 //allow user to run help
20 if(option == "help") { help(); abort = true; }
23 //valid paramters for this command
24 string Array[] = {"fasta","filter","correction","processors","window","increment","outputdir","inputdir"};
25 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
27 OptionParser parser(option);
28 map<string,string> parameters = parser.getParameters();
30 ValidParameters validParameter("chimera.bellerophon");
31 map<string,string>::iterator it;
33 //check to make sure all parameters are valid for command
34 for (it = parameters.begin(); it != parameters.end(); it++) {
35 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
38 //if the user changes the input directory command factory will send this info to us in the output parameter
39 string inputDir = validParameter.validFile(parameters, "inputdir", false);
40 if (inputDir == "not found"){ inputDir = ""; }
42 fastafile = validParameter.validFile(parameters, "fasta", false);
43 if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon command."); m->mothurOutEndLine(); abort = true; }
45 m->splitAtDash(fastafile, fastaFileNames);
47 //go through files and make sure they are good, if not, then disregard them
48 for (int i = 0; i < fastaFileNames.size(); i++) {
50 string path = m->hasPath(fastaFileNames[i]);
51 //if the user has not given a path then, add inputdir. else leave path alone.
52 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
58 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
60 //if you can't open it, try default location
61 if (ableToOpen == 1) {
62 if (m->getDefaultPath() != "") { //default path is set
63 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
64 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
65 ableToOpen = m->openInputFile(tryPath, in, "noerror");
66 fastaFileNames[i] = tryPath;
71 if (ableToOpen == 1) {
72 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
73 //erase from file list
74 fastaFileNames.erase(fastaFileNames.begin()+i);
80 //make sure there is at least one valid file left
81 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
84 //if the user changes the output directory command factory will send this info to us in the output parameter
85 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
87 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
91 temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
92 filter = m->isTrue(temp);
94 temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
95 correction = m->isTrue(temp);
97 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
98 convert(temp, processors);
100 temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
101 convert(temp, window);
103 temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
104 convert(temp, increment);
107 catch(exception& e) {
108 m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
112 //**********************************************************************************************************************
114 void ChimeraBellerophonCommand::help(){
116 m->mothurOut("The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n");
117 m->mothurOut("The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required.\n");
118 m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
119 m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n");
120 m->mothurOut("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");
121 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
123 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
125 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n");
126 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n");
127 m->mothurOut("chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n");
128 m->mothurOut("Example: chimera.bellerophon(fasta=AD.align, filter=True, correction=true, window=200) \n");
129 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
131 catch(exception& e) {
132 m->errorOut(e, "ChimeraBellerophonCommand", "help");
137 //***************************************************************************************************************
139 ChimeraBellerophonCommand::~ChimeraBellerophonCommand(){ /* do nothing */ }
141 //***************************************************************************************************************
143 int ChimeraBellerophonCommand::execute(){
146 if (abort == true) { return 0; }
148 for (int i = 0; i < fastaFileNames.size(); i++) {
150 m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
152 int start = time(NULL);
154 chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);
156 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.chimeras";
157 string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
159 chimera->getChimeras();
161 if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
165 MPI_File outMPIAccnos;
167 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
169 char outFilename[1024];
170 strcpy(outFilename, accnosFileName.c_str());
173 strcpy(FileName, outputFileName.c_str());
175 MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI); //comm, filename, mode, info, filepointer
176 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
178 numSeqs = chimera->print(outMPI, outMPIAccnos);
180 MPI_File_close(&outMPI);
181 MPI_File_close(&outMPIAccnos);
186 m->openOutputFile(outputFileName, out);
189 m->openOutputFile(accnosFileName, out2);
191 numSeqs = chimera->print(out, out2);
197 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete chimera; return 0; }
199 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
201 outputNames.push_back(outputFileName);
202 outputNames.push_back(accnosFileName);
207 m->mothurOutEndLine();
208 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
209 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
210 m->mothurOutEndLine();
215 catch(exception& e) {
216 m->errorOut(e, "ChimeraBellerophonCommand", "execute");
220 //**********************************************************************************************************************