X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=shhhercommand.cpp;h=4a6e5ff2375ce40560db1aa706edbdacefac0e0d;hp=3c467936a38fbecc55034979a9211ee89c7241b6;hb=615301e57c25e241356a9c2380648d117709458d;hpb=96f25c3c0f3ba2a1634094de146630dbc9ee0d03 diff --git a/shhhercommand.cpp b/shhhercommand.cpp index 3c46793..4a6e5ff 100644 --- a/shhhercommand.cpp +++ b/shhhercommand.cpp @@ -9,29 +9,20 @@ #include "shhhercommand.h" -#include "readcolumn.h" -#include "readmatrix.hpp" -#include "rabundvector.hpp" -#include "sabundvector.hpp" -#include "listvector.hpp" -#include "cluster.hpp" -#include "sparsematrix.hpp" -#include - //********************************************************************************************************************** vector ShhherCommand::setParameters(){ try { - CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow); - CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile); - CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plookup); - CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter); - CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma); - CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta); - CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pflow); + CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pfile); + CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(plookup); + CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pcutoff); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pmaxiter); + CommandParameter plarge("large", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(plarge); + CommandParameter psigma("sigma", "Number", "", "60", "", "", "","",false,false); parameters.push_back(psigma); + CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "","",false,false); parameters.push_back(pmindelta); + CommandParameter porder("order", "Multiple", "A-B-I", "A", "", "", "","",false,false, true); parameters.push_back(porder); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -47,6 +38,11 @@ string ShhherCommand::getHelpString(){ try { string helpString = ""; helpString += "The shhh.flows command reads a file containing flowgrams and creates a file of corrected sequences.\n"; + helpString += "The shhh.flows command parameters are flow, file, lookup, cutoff, processors, large, maxiter, sigma, mindelta and order.\n"; + helpString += "The flow parameter is used to input your flow file.\n"; + helpString += "The file parameter is used to input the *flow.files file created by trim.flows.\n"; + helpString += "The lookup parameter is used specify the lookup file you would like to use. http://www.mothur.org/wiki/Lookup_files.\n"; + helpString += "The order parameter options are A, B or I. Default=A. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"; return helpString; } catch(exception& e) { @@ -55,6 +51,25 @@ string ShhherCommand::getHelpString(){ } } //********************************************************************************************************************** +string ShhherCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],shhh.fasta"; } + else if (type == "name") { pattern = "[filename],shhh.names"; } + else if (type == "group") { pattern = "[filename],shhh.groups"; } + else if (type == "counts") { pattern = "[filename],shhh.counts"; } + else if (type == "qfile") { pattern = "[filename],shhh.qual"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** ShhherCommand::ShhherCommand(){ try { @@ -62,8 +77,12 @@ ShhherCommand::ShhherCommand(){ setParameters(); //initialize outputTypes -// vector tempOutNames; -// outputTypes["pn.dist"] = tempOutNames; + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["counts"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; } catch(exception& e) { @@ -76,18 +95,15 @@ ShhherCommand::ShhherCommand(){ ShhherCommand::ShhherCommand(string option) { try { - + #ifdef USE_MPI MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are MPI_Comm_size(MPI_COMM_WORLD, &ncpus); - + if(pid == 0){ #endif - - abort = false; calledHelp = false; - //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } else if(option == "citation") { citation(); abort = true; calledHelp = true;} @@ -107,9 +123,13 @@ ShhherCommand::ShhherCommand(string option) { } //initialize outputTypes - vector tempOutNames; -// outputTypes["pn.dist"] = tempOutNames; - // outputTypes["fasta"] = tempOutNames; + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["counts"] = tempOutNames; + outputTypes["qfile"] = 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); @@ -140,13 +160,15 @@ ShhherCommand::ShhherCommand(string option) { if (path == "") { parameters["file"] = inputDir + it->second; } } } - - + + //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 = ""; } + //check for required parameters flowFileName = validParameter.validFile(parameters, "flow", true); flowFilesFileName = validParameter.validFile(parameters, "file", true); if (flowFileName == "not found" && flowFilesFileName == "not found") { - m->mothurOut("values for either flow or file must be provided for the shhh.seqs command."); + m->mothurOut("values for either flow or file must be provided for the shhh.flows command."); m->mothurOutEndLine(); abort = true; } @@ -158,30 +180,103 @@ ShhherCommand::ShhherCommand(string option) { } else{ ofstream temp; - - //flow.files = 9 character offset - compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta"; + + string thisoutputDir = outputDir; + if (outputDir == "") { thisoutputDir = m->hasPath(flowFilesFileName); } //if user entered a file with a path then preserve it + + //we want to rip off .files, and also .flow if its there + string fileroot = m->getRootName(m->getSimpleName(flowFilesFileName)); + if (fileroot[fileroot.length()-1] == '.') { fileroot = fileroot.substr(0, fileroot.length()-1); } //rip off dot + string extension = m->getExtension(fileroot); + if (extension == ".flow") { fileroot = m->getRootName(fileroot); } + else { fileroot += "."; } //add back if needed + + compositeFASTAFileName = thisoutputDir + fileroot + "shhh.fasta"; m->openOutputFile(compositeFASTAFileName, temp); temp.close(); - compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names"; + compositeNamesFileName = thisoutputDir + fileroot + "shhh.names"; m->openOutputFile(compositeNamesFileName, temp); temp.close(); } - - //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 = ""; - outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it - } - - + + if(flowFilesFileName != "not found"){ + string fName; + + ifstream flowFilesFile; + m->openInputFile(flowFilesFileName, flowFilesFile); + while(flowFilesFile){ + fName = m->getline(flowFilesFile); + + //test if file is valid + ifstream in; + int ableToOpen = m->openInputFile(fName, in, "noerror"); + in.close(); + if (ableToOpen == 1) { + if (inputDir != "") { //default path is set + string tryPath = inputDir + fName; + m->mothurOut("Unable to open " + fName + ". Trying input directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fName = tryPath; + } + } + + if (ableToOpen == 1) { + if (m->getDefaultPath() != "") { //default path is set + string tryPath = m->getDefaultPath() + m->getSimpleName(fName); + m->mothurOut("Unable to open " + fName + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fName = tryPath; + } + } + + //if you can't open it its not in current working directory or inputDir, try mothur excutable location + if (ableToOpen == 1) { + string exepath = m->argv; + string tempPath = exepath; + for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); } + exepath = exepath.substr(0, (tempPath.find_last_of('m'))); + + string tryPath = m->getFullPathName(exepath) + m->getSimpleName(fName); + m->mothurOut("Unable to open " + fName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fName = tryPath; + } + + if (ableToOpen == 1) { m->mothurOut("Unable to open " + fName + ". Disregarding. "); m->mothurOutEndLine(); } + else { flowFileVector.push_back(fName); } + m->gobble(flowFilesFile); + } + flowFilesFile.close(); + if (flowFileVector.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; } + } + else{ + if (outputDir == "") { outputDir = m->hasPath(flowFileName); } + flowFileVector.push_back(flowFileName); + } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... string temp; temp = validParameter.validFile(parameters, "lookup", true); if (temp == "not found") { - lookupFileName = "LookUp_Titanium.pat"; + string path = m->argv; + string tempPath = path; + for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); } + path = path.substr(0, (tempPath.find_last_of('m'))); + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + path += "lookupFiles/"; +#else + path += "lookupFiles\\"; +#endif + lookupFileName = m->getFullPathName(path) + "LookUp_Titanium.pat"; int ableToOpen; ifstream in; @@ -191,7 +286,7 @@ ShhherCommand::ShhherCommand(string option) { //if you can't open it, try input location if (ableToOpen == 1) { if (inputDir != "") { //default path is set - string tryPath = inputDir + lookupFileName; + string tryPath = inputDir + m->getSimpleName(lookupFileName); m->mothurOut("Unable to open " + lookupFileName + ". Trying input directory " + tryPath); m->mothurOutEndLine(); ifstream in2; ableToOpen = m->openInputFile(tryPath, in2, "noerror"); @@ -239,7 +334,7 @@ ShhherCommand::ShhherCommand(string option) { for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); } exepath = exepath.substr(0, (tempPath.find_last_of('m'))); - string tryPath = m->getFullPathName(exepath) + lookupFileName; + string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName); m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine(); ifstream in2; int ableToOpen = m->openInputFile(tryPath, in2, "noerror"); @@ -251,32 +346,50 @@ ShhherCommand::ShhherCommand(string option) { temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.01"; } - convert(temp, cutoff); + m->mothurConvert(temp, cutoff); temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){ temp = "0.000001"; } - convert(temp, minDelta); + m->mothurConvert(temp, minDelta); temp = validParameter.validFile(parameters, "maxiter", false); if (temp == "not found"){ temp = "1000"; } - convert(temp, maxIters); + m->mothurConvert(temp, maxIters); + + temp = validParameter.validFile(parameters, "large", false); if (temp == "not found"){ temp = "0"; } + m->mothurConvert(temp, largeSize); + if (largeSize != 0) { large = true; } + else { large = false; } + if (largeSize < 0) { m->mothurOut("The value of the large cannot be negative.\n"); } + +#ifdef USE_MPI + if (large) { m->mothurOut("The large parameter is not available with the MPI-Enabled version.\n"); large=false; } +#endif + temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found") { temp = "60"; } - convert(temp, sigma); - - flowOrder = validParameter.validFile(parameters, "order", false); - if (flowOrder == "not found"){ flowOrder = "TACG"; } - else if(flowOrder.length() != 4){ - m->mothurOut("The value of the order option must be four bases long\n"); - } + m->mothurConvert(temp, sigma); + + temp = validParameter.validFile(parameters, "order", false); if (temp == "not found"){ temp = "A"; } + if (temp.length() > 1) { m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true; + } + else { + if (toupper(temp[0]) == 'A') { flowOrder = "TACG"; } + else if(toupper(temp[0]) == 'B'){ + flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC"; } + else if(toupper(temp[0]) == 'I'){ + flowOrder = "TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC"; } + else { + m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true; + } + } + } - #ifdef USE_MPI } #endif - } catch(exception& e) { m->errorOut(e, "ShhherCommand", "ShhherCommand"); @@ -291,7 +404,7 @@ int ShhherCommand::execute(){ int tag = 1976; MPI_Status status; - + if(pid == 0){ for(int i=1;icontrol_pressed) { return 0; } getJointLookUp(); if (m->control_pressed) { return 0; } - vector flowFileVector; + vector flowFileVector; if(flowFilesFileName != "not found"){ string fName; - + ifstream flowFilesFile; m->openInputFile(flowFilesFileName, flowFilesFile); while(flowFilesFile){ @@ -320,6 +433,7 @@ int ShhherCommand::execute(){ else{ flowFileVector.push_back(flowFileName); } + int numFiles = flowFileVector.size(); for(int i=1;icontrol_pressed) { break; } + + getOTUData(listFileName); m->mothurRemove(distFileName); @@ -398,6 +514,7 @@ int ShhherCommand::execute(){ if (m->control_pressed) { break; } + for(int i=1;imothurOutEndLine(); @@ -694,7 +811,37 @@ int ShhherCommand::execute(){ exit(1); } } - +/**************************************************************************************************/ +string ShhherCommand::createNamesFile(){ + try{ + + vector duplicateNames(numUniques, ""); + for(int i=0;i variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName)); + string nameFileName = getOutputFileName("name",variables); + + ofstream nameFile; + m->openOutputFile(nameFileName, nameFile); + + for(int i=0;icontrol_pressed) { break; } + + // nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl; + nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl; + } + + nameFile.close(); + return nameFileName; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "createNamesFile"); + exit(1); + } +} /**************************************************************************************************/ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){ @@ -723,7 +870,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){ } } if(i % 100 == 0){ - m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); + m->mothurOutJustToScreen(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); } } @@ -732,7 +879,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){ if (m->control_pressed) { return fDistFileName; } - m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); + m->mothurOutJustToScreen(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n'); ofstream distFile(fDistFileName.c_str()); distFile << outStream.str(); @@ -741,424 +888,1651 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){ return fDistFileName; } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "flowDistParentFork"); + m->errorOut(e, "ShhherCommand", "flowDistMPI"); exit(1); } } +/**************************************************************************************************/ + +void ShhherCommand::getOTUData(string listFileName){ + try { + + ifstream listFile; + m->openInputFile(listFileName, listFile); + string label; + + listFile >> label >> numOTUs; + + otuData.assign(numSeqs, 0); + cumNumSeqs.assign(numOTUs, 0); + nSeqsPerOTU.assign(numOTUs, 0); + aaP.clear();aaP.resize(numOTUs); + + seqNumber.clear(); + aaI.clear(); + seqIndex.clear(); + + string singleOTU = ""; + + for(int i=0;icontrol_pressed) { break; } + + listFile >> singleOTU; + + istringstream otuString(singleOTU); + + while(otuString){ + + string seqName = ""; + + for(int j=0;j::iterator nmIt = nameMap.find(seqName); + int index = nmIt->second; + + nameMap.erase(nmIt); + + otuData[index] = i; + nSeqsPerOTU[i]++; + aaP[i].push_back(index); + seqName = ""; + } + } + + map::iterator nmIt = nameMap.find(seqName); + + int index = nmIt->second; + nameMap.erase(nmIt); + + otuData[index] = i; + nSeqsPerOTU[i]++; + aaP[i].push_back(index); + + otuString.get(); + } + + sort(aaP[i].begin(), aaP[i].end()); + for(int j=0;jerrorOut(e, "ShhherCommand", "getOTUData"); + exit(1); + } +} -#else -//********************************************************************************************************************** - -int ShhherCommand::execute(){ - try { - if (abort == true) { return 0; } - - getSingleLookUp(); if (m->control_pressed) { return 0; } - getJointLookUp(); if (m->control_pressed) { return 0; } - - - vector flowFileVector; - if(flowFilesFileName != "not found"){ - string fName; - - ifstream flowFilesFile; - m->openInputFile(flowFilesFileName, flowFilesFile); - while(flowFilesFile){ - fName = m->getline(flowFilesFile); - flowFileVector.push_back(fName); - m->gobble(flowFilesFile); - } - } - else{ - flowFileVector.push_back(flowFileName); - } - int numFiles = flowFileVector.size(); - - - for(int i=0;icontrol_pressed) { break; } - - flowFileName = flowFileVector[i]; - - m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n"); - m->mothurOut("Reading flowgrams...\n"); - getFlowData(); - - if (m->control_pressed) { break; } - - m->mothurOut("Identifying unique flowgrams...\n"); - getUniques(); - - if (m->control_pressed) { break; } - - m->mothurOut("Calculating distances between flowgrams...\n"); - string distFileName = createDistFile(processors); - string namesFileName = createNamesFile(); - - if (m->control_pressed) { break; } - - m->mothurOut("\nClustering flowgrams...\n"); - string listFileName = cluster(distFileName, namesFileName); - - if (m->control_pressed) { break; } - - getOTUData(listFileName); - - if (m->control_pressed) { break; } - - m->mothurRemove(distFileName); - m->mothurRemove(namesFileName); - m->mothurRemove(listFileName); - - initPyroCluster(); - - if (m->control_pressed) { break; } - - double maxDelta = 0; - int iter = 0; - - double begClock = clock(); - unsigned long long begTime = time(NULL); - - m->mothurOut("\nDenoising flowgrams...\n"); - m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n"); - - while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){ - - if (m->control_pressed) { break; } - - double cycClock = clock(); - unsigned long long cycTime = time(NULL); - fill(); - - if (m->control_pressed) { break; } - - calcCentroids(); - - if (m->control_pressed) { break; } - - maxDelta = getNewWeights(); if (m->control_pressed) { break; } - double nLL = getLikelihood(); if (m->control_pressed) { break; } - checkCentroids(); - - if (m->control_pressed) { break; } - - calcNewDistances(); - - if (m->control_pressed) { break; } - - iter++; - - m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n'); +/**************************************************************************************************/ - } - - if (m->control_pressed) { break; } - - m->mothurOut("\nFinalizing...\n"); - fill(); - - if (m->control_pressed) { break; } - - setOTUs(); - - if (m->control_pressed) { break; } - - vector otuCounts(numOTUs, 0); - for(int i=0;icontrol_pressed) { break; } - writeQualities(otuCounts); if (m->control_pressed) { break; } - writeSequences(otuCounts); if (m->control_pressed) { break; } - writeNames(otuCounts); if (m->control_pressed) { break; } - writeClusters(otuCounts); if (m->control_pressed) { break; } - writeGroups(); if (m->control_pressed) { break; } - - m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n'); - } - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } +void ShhherCommand::initPyroCluster(){ + try{ + if (numOTUs < processors) { processors = 1; } + + if (m->debug) { m->mothurOut("[DEBUG]: numSeqs = " + toString(numSeqs) + " numOTUS = " + toString(numOTUs) + " about to alloc a dist vector with size = " + toString((numSeqs * numOTUs)) + ".\n"); } + + dist.assign(numSeqs * numOTUs, 0); + change.assign(numOTUs, 1); + centroids.assign(numOTUs, -1); + weight.assign(numOTUs, 0); + singleTau.assign(numSeqs, 1.0); + + nSeqsBreaks.assign(processors+1, 0); + nOTUsBreaks.assign(processors+1, 0); + + if (m->debug) { m->mothurOut("[DEBUG]: made it through the memory allocation.\n"); } + + nSeqsBreaks[0] = 0; + for(int i=0;ierrorOut(e, "ShhherCommand", "initPyroCluster"); + exit(1); + } +} - - if(compositeFASTAFileName != ""){ - outputNames.push_back(compositeFASTAFileName); - outputNames.push_back(compositeNamesFileName); - } +/**************************************************************************************************/ - m->mothurOutEndLine(); - m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } - m->mothurOutEndLine(); - - return 0; - } - catch(exception& e) { - m->errorOut(e, "ShhherCommand", "execute"); - exit(1); - } +void ShhherCommand::fill(){ + try { + int index = 0; + for(int i=0;icontrol_pressed) { break; } + + cumNumSeqs[i] = index; + for(int j=0;jerrorOut(e, "ShhherCommand", "fill"); + exit(1); + } } -#endif -/**************************************************************************************************/ +/**************************************************************************************************/ + void ShhherCommand::getFlowData(){ + try{ + ifstream flowFile; + m->openInputFile(flowFileName, flowFile); + + string seqName; + seqNameVector.clear(); + lengths.clear(); + flowDataIntI.clear(); + nameMap.clear(); + + + int currentNumFlowCells; + + float intensity; + + string numFlowTest; + flowFile >> numFlowTest; + + if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); } + else { convert(numFlowTest, numFlowCells); } + + int index = 0;//pcluster + while(!flowFile.eof()){ + + if (m->control_pressed) { break; } + + flowFile >> seqName >> currentNumFlowCells; + lengths.push_back(currentNumFlowCells); + + seqNameVector.push_back(seqName); + nameMap[seqName] = index++;//pcluster + + for(int i=0;i> intensity; + if(intensity > 9.99) { intensity = 9.99; } + int intI = int(100 * intensity + 0.0001); + flowDataIntI.push_back(intI); + } + m->gobble(flowFile); + } + flowFile.close(); + + numSeqs = seqNameVector.size(); + + for(int i=0;icontrol_pressed) { break; } + + int iNumFlowCells = i * numFlowCells; + for(int j=lengths[i];jerrorOut(e, "ShhherCommand", "getFlowData"); + exit(1); + } +} +/**************************************************************************************************/ +void ShhherCommand::calcNewDistancesChildMPI(int startSeq, int stopSeq, vector& otuIndex){ + try{ - ifstream flowFile; - m->openInputFile(flowFileName, flowFile); - - string seqName; - seqNameVector.clear(); - lengths.clear(); - flowDataIntI.clear(); - nameMap.clear(); - - - int currentNumFlowCells; - - float intensity; + vector newTau(numOTUs,0); + vector norms(numSeqs, 0); + otuIndex.clear(); + seqIndex.clear(); + singleTau.clear(); - flowFile >> numFlowCells; - int index = 0;//pcluster - while(!flowFile.eof()){ + for(int i=startSeq;icontrol_pressed) { break; } - flowFile >> seqName >> currentNumFlowCells; - lengths.push_back(currentNumFlowCells); - - seqNameVector.push_back(seqName); - nameMap[seqName] = index++;//pcluster - - for(int i=0;i> intensity; - if(intensity > 9.99) { intensity = 9.99; } - int intI = int(100 * intensity + 0.0001); - flowDataIntI.push_back(intI); + double offset = 1e8; + int indexOffset = i * numOTUs; + + for(int j=0;j MIN_WEIGHT && change[j] == 1){ + dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]); + } + if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){ + offset = dist[indexOffset + j]; + } } - m->gobble(flowFile); - } - flowFile.close(); - - numSeqs = seqNameVector.size(); - - for(int i=0;icontrol_pressed) { break; } + for(int j=0;j MIN_WEIGHT){ + newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j]; + norms[i] += newTau[j]; + } + else{ + newTau[j] = 0.0; + } + } - int iNumFlowCells = i * numFlowCells; - for(int j=lengths[i];j MIN_TAU){ + otuIndex.push_back(j); + seqIndex.push_back(i); + singleTau.push_back(newTau[j]); + } } + } - } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "getFlowData"); - exit(1); - } + m->errorOut(e, "ShhherCommand", "calcNewDistancesChildMPI"); + exit(1); + } } /**************************************************************************************************/ -void ShhherCommand::getSingleLookUp(){ - try{ - // these are the -log probabilities that a signal corresponds to a particular homopolymer length - singleLookUp.assign(HOMOPS * NUMBINS, 0); - - int index = 0; - ifstream lookUpFile; - m->openInputFile(lookupFileName, lookUpFile); - - for(int i=0;icontrol_pressed) { break; } - - float logFracFreq; - lookUpFile >> logFracFreq; - - for(int j=0;j> singleLookUp[index]; - index++; - } - } - lookUpFile.close(); - } - catch(exception& e) { - m->errorOut(e, "ShhherCommand", "getSingleLookUp"); - exit(1); - } +void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){ + + try{ + + int total = 0; + vector newTau(numOTUs,0); + vector norms(numSeqs, 0); + nSeqsPerOTU.assign(numOTUs, 0); + + for(int i=startSeq;icontrol_pressed) { break; } + + int indexOffset = i * numOTUs; + + double offset = 1e8; + + for(int j=0;j MIN_WEIGHT && change[j] == 1){ + dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]); + } + + if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){ + offset = dist[indexOffset + j]; + } + } + + for(int j=0;j MIN_WEIGHT){ + newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j]; + norms[i] += newTau[j]; + } + else{ + newTau[j] = 0.0; + } + } + + for(int j=0;j MIN_TAU){ + + int oldTotal = total; + + total++; + + singleTau.resize(total, 0); + seqNumber.resize(total, 0); + seqIndex.resize(total, 0); + + singleTau[oldTotal] = newTau[j]; + + aaP[j][nSeqsPerOTU[j]] = oldTotal; + aaI[j][nSeqsPerOTU[j]] = i; + nSeqsPerOTU[j]++; + } + } + + } + + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "calcNewDistancesParent"); + exit(1); + } } /**************************************************************************************************/ -void ShhherCommand::getJointLookUp(){ - try{ +void ShhherCommand::setOTUs(){ + + try { + vector bigTauMatrix(numOTUs * numSeqs, 0.0000); + + for(int i=0;icontrol_pressed) { break; } + + for(int j=0;j maxTau){ + maxTau = bigTauMatrix[i * numOTUs + j]; + maxOTU = j; + } + } + + otuData[i] = maxOTU; + } + + nSeqsPerOTU.assign(numOTUs, 0); + + for(int i=0;ierrorOut(e, "ShhherCommand", "setOTUs"); + exit(1); + } +} + +/**************************************************************************************************/ + +void ShhherCommand::getUniques(){ + try{ + + + numUniques = 0; + uniqueFlowgrams.assign(numFlowCells * numSeqs, -1); + uniqueCount.assign(numSeqs, 0); // anWeights + uniqueLengths.assign(numSeqs, 0); + mapSeqToUnique.assign(numSeqs, -1); + mapUniqueToSeq.assign(numSeqs, -1); + + vector uniqueFlowDataIntI(numFlowCells * numSeqs, -1); + + for(int i=0;icontrol_pressed) { break; } + + int index = 0; + + vector current(numFlowCells); + for(int j=0;j uniqueLengths[j]) { uniqueLengths[j] = lengths[i]; } + break; + } + index++; + } + + if(index == numUniques){ + uniqueLengths[numUniques] = lengths[i]; + uniqueCount[numUniques] = 1; + mapSeqToUnique[i] = numUniques;//anMap + mapUniqueToSeq[numUniques] = i;//anF + + for(int k=0;kcontrol_pressed) { break; } flowDataPrI[i] = getProbIntensity(flowDataIntI[i]); } + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "getUniques"); + exit(1); + } +} + +/**************************************************************************************************/ + +float ShhherCommand::calcPairwiseDist(int seqA, int seqB){ + try{ + int minLength = lengths[mapSeqToUnique[seqA]]; + if(lengths[seqB] < minLength){ minLength = lengths[mapSeqToUnique[seqB]]; } + + int ANumFlowCells = seqA * numFlowCells; + int BNumFlowCells = seqB * numFlowCells; + + float dist = 0; + + for(int i=0;icontrol_pressed) { break; } + + int flowAIntI = flowDataIntI[ANumFlowCells + i]; + float flowAPrI = flowDataPrI[ANumFlowCells + i]; + + int flowBIntI = flowDataIntI[BNumFlowCells + i]; + float flowBPrI = flowDataPrI[BNumFlowCells + i]; + dist += jointLookUp[flowAIntI * NUMBINS + flowBIntI] - flowAPrI - flowBPrI; + } + + dist /= (float) minLength; + return dist; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "calcPairwiseDist"); + exit(1); + } +} + +//**********************************************************************************************************************/ + +string ShhherCommand::cluster(string distFileName, string namesFileName){ + try { + + ReadMatrix* read = new ReadColumnMatrix(distFileName); + read->setCutoff(cutoff); - // the most likely joint probability (-log) that two intenities have the same polymer length - jointLookUp.resize(NUMBINS * NUMBINS, 0); + NameAssignment* clusterNameMap = new NameAssignment(namesFileName); + clusterNameMap->readMap(); + read->read(clusterNameMap); + + ListVector* list = read->getListVector(); + SparseDistanceMatrix* matrix = read->getDMatrix(); - for(int i=0;icontrol_pressed) { break; } - - for(int j=0;jerrorOut(e, "ShhherCommand", "getJointLookUp"); - exit(1); - } + delete read; + delete clusterNameMap; + + RAbundVector* rabund = new RAbundVector(list->getRAbundVector()); + + Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest"); + string tag = cluster->getTag(); + + double clusterCutoff = cutoff; + while (matrix->getSmallDist() <= clusterCutoff && matrix->getNNodes() > 0){ + + if (m->control_pressed) { break; } + + cluster->update(clusterCutoff); + } + + list->setLabel(toString(cutoff)); + + string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.list"; + ofstream listFile; + m->openOutputFile(listFileName, listFile); + list->print(listFile); + listFile.close(); + + delete matrix; delete cluster; delete rabund; delete list; + + return listFileName; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "cluster"); + exit(1); + } } /**************************************************************************************************/ -double ShhherCommand::getProbIntensity(int intIntensity){ - try{ +void ShhherCommand::calcCentroidsDriver(int start, int finish){ + + //this function gets the most likely homopolymer length at a flow position for a group of sequences + //within an otu + + try{ + + for(int i=start;icontrol_pressed) { break; } + + double count = 0; + int position = 0; + int minFlowGram = 100000000; + double minFlowValue = 1e8; + change[i] = 0; //FALSE + + for(int j=0;j 0 && count > MIN_COUNT){ + vector adF(nSeqsPerOTU[i]); + vector anL(nSeqsPerOTU[i]); + + for(int j=0;jerrorOut(e, "ShhherCommand", "calcCentroidsDriver"); + exit(1); + } +} + +/**************************************************************************************************/ + +double ShhherCommand::getDistToCentroid(int cent, int flow, int length){ + try{ + + int flowAValue = cent * numFlowCells; + int flowBValue = flow * numFlowCells; + + double dist = 0; + + for(int i=0;ierrorOut(e, "ShhherCommand", "getDistToCentroid"); + exit(1); + } +} + +/**************************************************************************************************/ + +double ShhherCommand::getNewWeights(){ + try{ + + double maxChange = 0; + + for(int i=0;icontrol_pressed) { break; } + + double difference = weight[i]; + weight[i] = 0; + + for(int j=0;j maxChange){ maxChange = difference; } + } + return maxChange; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "getNewWeights"); + exit(1); + } +} + + /**************************************************************************************************/ + +double ShhherCommand::getLikelihood(){ + + try{ + + vector P(numSeqs, 0); + int effNumOTUs = 0; + + for(int i=0;i MIN_WEIGHT){ + effNumOTUs++; + } + } + + string hold; + for(int i=0;icontrol_pressed) { break; } + + for(int j=0;jerrorOut(e, "ShhherCommand", "getNewWeights"); + exit(1); + } +} + +/**************************************************************************************************/ + +void ShhherCommand::checkCentroids(){ + try{ + vector unique(numOTUs, 1); + + for(int i=0;icontrol_pressed) { break; } + + if(unique[i] == 1){ + for(int j=i+1;jerrorOut(e, "ShhherCommand", "checkCentroids"); + exit(1); + } +} + /**************************************************************************************************/ - double minNegLogProb = 100000000; + +void ShhherCommand::writeQualities(vector otuCounts){ + + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName)); + string qualityFileName = getOutputFileName("qfile",variables); + + ofstream qualityFile; + m->openOutputFile(qualityFileName, qualityFile); + + qualityFile.setf(ios::fixed, ios::floatfield); + qualityFile.setf(ios::showpoint); + qualityFile << setprecision(6); + + vector > qualities(numOTUs); + vector pr(HOMOPS, 0); + + + for(int i=0;icontrol_pressed) { break; } + + int index = 0; + int base = 0; + + if(nSeqsPerOTU[i] > 0){ + qualities[i].assign(1024, -1); + + while(index < numFlowCells){ + double maxPrValue = 1e8; + short maxPrIndex = -1; + double count = 0.0000; + + pr.assign(HOMOPS, 0); + + for(int j=0;j MIN_COUNT){ + double U = 0.0000; + double norm = 0.0000; + + for(int s=0;s0.00){ + temp = log10(U); + } + else{ + temp = -10.1; + } + temp = floor(-10 * temp); + value = (int)floor(temp); + if(value > 100){ value = 100; } + + qualities[i][base] = (int)value; + base++; + } + } + + index++; + } + } + + + if(otuCounts[i] > 0){ + qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl; + + int j=4; //need to get past the first four bases + while(qualities[i][j] != -1){ + qualityFile << qualities[i][j] << ' '; + j++; + } + qualityFile << endl; + } + } + qualityFile.close(); + outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName); + + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "writeQualities"); + exit(1); + } +} + +/**************************************************************************************************/ + +void ShhherCommand::writeSequences(vector otuCounts){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string fastaFileName = getOutputFileName("fasta",variables); + ofstream fastaFile; + m->openOutputFile(fastaFileName, fastaFile); + + vector names(numOTUs, ""); + + for(int i=0;icontrol_pressed) { break; } + + int index = centroids[i]; + + if(otuCounts[i] > 0){ + fastaFile << '>' << seqNameVector[aaI[i][0]] << endl; + + string newSeq = ""; + + for(int j=0;jappendFiles(fastaFileName, compositeFASTAFileName); + } + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "writeSequences"); + exit(1); + } +} + +/**************************************************************************************************/ + +void ShhherCommand::writeNames(vector otuCounts){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string nameFileName = getOutputFileName("name",variables); + ofstream nameFile; + m->openOutputFile(nameFileName, nameFile); + + for(int i=0;icontrol_pressed) { break; } + + if(otuCounts[i] > 0){ + nameFile << seqNameVector[aaI[i][0]] << '\t' << seqNameVector[aaI[i][0]]; + + for(int j=1;jappendFiles(nameFileName, compositeNamesFileName); + } + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "writeNames"); + exit(1); + } +} + +/**************************************************************************************************/ + +void ShhherCommand::writeGroups(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } + string fileRoot = m->getRootName(m->getSimpleName(flowFileName)); + int pos = fileRoot.find_first_of('.'); + string fileGroup = fileRoot; + if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); } + map variables; + variables["[filename]"] = thisOutputDir + fileRoot; + string groupFileName = getOutputFileName("group",variables); + ofstream groupFile; + m->openOutputFile(groupFileName, groupFile); + + for(int i=0;icontrol_pressed) { break; } + groupFile << seqNameVector[i] << '\t' << fileGroup << endl; + } + groupFile.close(); + outputNames.push_back(groupFileName); outputTypes["group"].push_back(groupFileName); + + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "writeGroups"); + exit(1); + } +} + +/**************************************************************************************************/ + +void ShhherCommand::writeClusters(vector otuCounts){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string otuCountsFileName = getOutputFileName("counts",variables); + ofstream otuCountsFile; + m->openOutputFile(otuCountsFileName, otuCountsFile); + + string bases = flowOrder; + + for(int i=0;icontrol_pressed) { + break; + } + //output the translated version of the centroid sequence for the otu + if(otuCounts[i] > 0){ + int index = centroids[i]; + + otuCountsFile << "ideal\t"; + for(int j=8;jerrorOut(e, "ShhherCommand", "writeClusters"); + exit(1); + } +} + +#else +//********************************************************************************************************************** + +int ShhherCommand::execute(){ + try { + if (abort == true) { if (calledHelp) { return 0; } return 2; } - for(int i=0;icontrol_pressed) { break; } - - float negLogProb = singleLookUp[i * NUMBINS + intIntensity]; - if(negLogProb < minNegLogProb) { minNegLogProb = negLogProb; } + getSingleLookUp(); if (m->control_pressed) { return 0; } + getJointLookUp(); if (m->control_pressed) { return 0; } + + int numFiles = flowFileVector.size(); + + if (numFiles < processors) { processors = numFiles; } + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + if (processors == 1) { driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName); } + else { createProcesses(flowFileVector); } //each processor processes one file +#else + driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName); +#endif + + if(compositeFASTAFileName != ""){ + outputNames.push_back(compositeFASTAFileName); outputTypes["fasta"].push_back(compositeFASTAFileName); + outputNames.push_back(compositeNamesFileName); outputTypes["name"].push_back(compositeNamesFileName); } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); - return minNegLogProb; + return 0; } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "getProbIntensity"); + m->errorOut(e, "ShhherCommand", "execute"); exit(1); } } - +#endif +//******************************************************************************************************************** +//sorts biggest to smallest +inline bool compareFileSizes(string left, string right){ + + FILE * pFile; + long leftsize = 0; + + //get num bytes in file + string filename = left; + pFile = fopen (filename.c_str(),"rb"); + string error = "Error opening " + filename; + if (pFile==NULL) perror (error.c_str()); + else{ + fseek (pFile, 0, SEEK_END); + leftsize=ftell (pFile); + fclose (pFile); + } + + FILE * pFile2; + long rightsize = 0; + + //get num bytes in file + filename = right; + pFile2 = fopen (filename.c_str(),"rb"); + error = "Error opening " + filename; + if (pFile2==NULL) perror (error.c_str()); + else{ + fseek (pFile2, 0, SEEK_END); + rightsize=ftell (pFile2); + fclose (pFile2); + } + + return (leftsize > rightsize); +} /**************************************************************************************************/ -void ShhherCommand::getUniques(){ - try{ +int ShhherCommand::createProcesses(vector filenames){ + try { + vector processIDS; + int process = 1; + int num = 0; + + //sanity check + if (filenames.size() < processors) { processors = filenames.size(); } + + //sort file names by size to divide load better + sort(filenames.begin(), filenames.end(), compareFileSizes); + + vector < vector > dividedFiles; //dividedFiles[1] = vector of filenames for process 1... + dividedFiles.resize(processors); + + //for each file, figure out which process will complete it + //want to divide the load intelligently so the big files are spread between processes + for (int i = 0; i < filenames.size(); i++) { + int processToAssign = (i+1) % processors; + if (processToAssign == 0) { processToAssign = processors; } + + dividedFiles[(processToAssign-1)].push_back(filenames[i]); + } + + //now lets reverse the order of ever other process, so we balance big files running with little ones + for (int i = 0; i < processors; i++) { + int remainder = ((i+1) % processors); + if (remainder) { reverse(dividedFiles[i].begin(), dividedFiles[i].end()); } + } + + + //divide the groups between the processors + /*vector lines; + vector numFilesToComplete; + int numFilesPerProcessor = filenames.size() / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numFilesPerProcessor; + int endIndex = (i+1) * numFilesPerProcessor; + if(i == (processors - 1)){ endIndex = filenames.size(); } + lines.push_back(linePair(startIndex, endIndex)); + numFilesToComplete.push_back((endIndex-startIndex)); + }*/ + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); + + if (pid > 0) { + processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later + process++; + }else if (pid == 0){ + num = driver(dividedFiles[process], compositeFASTAFileName + toString(getpid()) + ".temp", compositeNamesFileName + toString(getpid()) + ".temp"); + + //pass numSeqs to parent + ofstream out; + string tempFile = compositeFASTAFileName + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + out << num << endl; + out.close(); + + exit(0); + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } + } + //do my part + driver(dividedFiles[0], compositeFASTAFileName, compositeNamesFileName); - numUniques = 0; - uniqueFlowgrams.assign(numFlowCells * numSeqs, -1); - uniqueCount.assign(numSeqs, 0); // anWeights - uniqueLengths.assign(numSeqs, 0); - mapSeqToUnique.assign(numSeqs, -1); - mapUniqueToSeq.assign(numSeqs, -1); + //force parent to wait until all the processes are done + for (int i=0;i pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=0; i uniqueFlowDataIntI(numFlowCells * numSeqs, -1); + //using the main process as a worker saves time and memory + //do my part + driver(filenames, compositeFASTAFileName, compositeNamesFileName, lines[processors-1].start, lines[processors-1].end); - for(int i=0;icontrol_pressed) { break; } - - int index = 0; - - vector current(numFlowCells); - for(int j=0;j uniqueLengths[j]) { uniqueLengths[j] = lengths[i]; } - break; - } - index++; - } - - if(index == numUniques){ - uniqueLengths[numUniques] = lengths[i]; - uniqueCount[numUniques] = 1; - mapSeqToUnique[i] = numUniques;//anMap - mapUniqueToSeq[numUniques] = i;//anF - - for(int k=0;kcontrol_pressed) { break; } flowDataPrI[i] = getProbIntensity(flowDataIntI[i]); } - } + //Close all thread handles and free memory allocations. + for(int i=0; i < pDataArray.size(); i++){ + for(int j=0; j < pDataArray[i]->outputNames.size(); j++){ outputNames.push_back(pDataArray[i]->outputNames[j]); } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + */ + #endif + + for (int i=0;iopenInputFile(tempFile, in); + if (!in.eof()) { + int tempNum = 0; + in >> tempNum; + if (tempNum != dividedFiles[i+1].size()) { + m->mothurOut("[ERROR]: main process expected " + toString(processIDS[i]) + " to complete " + toString(dividedFiles[i+1].size()) + " files, and it only reported completing " + toString(tempNum) + ". This will cause file mismatches. The flow files may be too large to process with multiple processors. \n"); + } + } + in.close(); m->mothurRemove(tempFile); + + if (compositeFASTAFileName != "") { + m->appendFiles((compositeFASTAFileName + toString(processIDS[i]) + ".temp"), compositeFASTAFileName); + m->appendFiles((compositeNamesFileName + toString(processIDS[i]) + ".temp"), compositeNamesFileName); + m->mothurRemove((compositeFASTAFileName + toString(processIDS[i]) + ".temp")); + m->mothurRemove((compositeNamesFileName + toString(processIDS[i]) + ".temp")); + } + } + + return 0; + + } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "getUniques"); + m->errorOut(e, "ShhherCommand", "createProcesses"); exit(1); } } +/**************************************************************************************************/ +vector ShhherCommand::parseFlowFiles(string filename){ + try { + vector files; + int count = 0; + + ifstream in; + m->openInputFile(filename, in); + + int thisNumFLows = 0; + in >> thisNumFLows; m->gobble(in); + + while (!in.eof()) { + if (m->control_pressed) { break; } + + ofstream out; + string outputFileName = filename + toString(count) + ".temp"; + m->openOutputFile(outputFileName, out); + out << thisNumFLows << endl; + files.push_back(outputFileName); + + int numLinesWrote = 0; + for (int i = 0; i < largeSize; i++) { + if (in.eof()) { break; } + string line = m->getline(in); m->gobble(in); + out << line << endl; + numLinesWrote++; + } + out.close(); + + if (numLinesWrote == 0) { m->mothurRemove(outputFileName); files.pop_back(); } + count++; + } + in.close(); + + if (m->control_pressed) { for (int i = 0; i < files.size(); i++) { m->mothurRemove(files[i]); } files.clear(); } + + m->mothurOut("\nDivided " + filename + " into " + toString(files.size()) + " files.\n\n"); + + return files; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "parseFlowFiles"); + exit(1); + } +} /**************************************************************************************************/ -float ShhherCommand::calcPairwiseDist(int seqA, int seqB){ +int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFileName, string thisCompositeNamesFileName){ + try { + + int numCompleted = 0; + + for(int i=0;icontrol_pressed) { break; } + + vector theseFlowFileNames; theseFlowFileNames.push_back(filenames[i]); + if (large) { theseFlowFileNames = parseFlowFiles(filenames[i]); } + + if (m->control_pressed) { break; } + + double begClock = clock(); + unsigned long long begTime; + + string fileNameForOutput = filenames[i]; + + for (int g = 0; g < theseFlowFileNames.size(); g++) { + + string flowFileName = theseFlowFileNames[g]; + m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(filenames.size()) + ")\t<<<<<\n"); + m->mothurOut("Reading flowgrams...\n"); + + vector seqNameVector; + vector lengths; + vector flowDataIntI; + vector flowDataPrI; + map nameMap; + vector uniqueFlowgrams; + vector uniqueCount; + vector mapSeqToUnique; + vector mapUniqueToSeq; + vector uniqueLengths; + int numFlowCells; + + if (m->debug) { m->mothurOut("[DEBUG]: About to read flowgrams.\n"); } + int numSeqs = getFlowData(flowFileName, seqNameVector, lengths, flowDataIntI, nameMap, numFlowCells); + + if (m->control_pressed) { break; } + + m->mothurOut("Identifying unique flowgrams...\n"); + int numUniques = getUniques(numSeqs, numFlowCells, uniqueFlowgrams, uniqueCount, uniqueLengths, mapSeqToUnique, mapUniqueToSeq, lengths, flowDataPrI, flowDataIntI); + + if (m->control_pressed) { break; } + + m->mothurOut("Calculating distances between flowgrams...\n"); + string distFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist"; + begTime = time(NULL); + + + flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI); + + m->mothurOutEndLine(); + m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n'); + + + string namesFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names"; + createNamesFile(numSeqs, numUniques, namesFileName, seqNameVector, mapSeqToUnique, mapUniqueToSeq); + + if (m->control_pressed) { break; } + + m->mothurOut("\nClustering flowgrams...\n"); + string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.list"; + cluster(listFileName, distFileName, namesFileName); + + if (m->control_pressed) { break; } + + vector otuData; + vector cumNumSeqs; + vector nSeqsPerOTU; + vector > aaP; //tMaster->aanP: each row is a different otu / each col contains the sequence indices + vector > aaI; //tMaster->aanI: that are in each otu - can't differentiate between aaP and aaI + vector seqNumber; //tMaster->anP: the sequence id number sorted by OTU + vector seqIndex; //tMaster->anI; the index that corresponds to seqNumber + + + int numOTUs = getOTUData(numSeqs, listFileName, otuData, cumNumSeqs, nSeqsPerOTU, aaP, aaI, seqNumber, seqIndex, nameMap); + + if (m->control_pressed) { break; } + + m->mothurRemove(distFileName); + m->mothurRemove(namesFileName); + m->mothurRemove(listFileName); + + vector dist; //adDist - distance of sequences to centroids + vector change; //did the centroid sequence change? 0 = no; 1 = yes + vector centroids; //the representative flowgram for each cluster m + vector weight; + vector singleTau; //tMaster->adTau: 1-D Tau vector (1xnumSeqs) + vector nSeqsBreaks; + vector nOTUsBreaks; + + if (m->debug) { m->mothurOut("[DEBUG]: numSeqs = " + toString(numSeqs) + " numOTUS = " + toString(numOTUs) + " about to alloc a dist vector with size = " + toString((numSeqs * numOTUs)) + ".\n"); } + + dist.assign(numSeqs * numOTUs, 0); + change.assign(numOTUs, 1); + centroids.assign(numOTUs, -1); + weight.assign(numOTUs, 0); + singleTau.assign(numSeqs, 1.0); + + nSeqsBreaks.assign(2, 0); + nOTUsBreaks.assign(2, 0); + + nSeqsBreaks[0] = 0; + nSeqsBreaks[1] = numSeqs; + nOTUsBreaks[1] = numOTUs; + + if (m->debug) { m->mothurOut("[DEBUG]: done allocating memory, about to denoise.\n"); } + + if (m->control_pressed) { break; } + + double maxDelta = 0; + int iter = 0; + + begClock = clock(); + begTime = time(NULL); + + m->mothurOut("\nDenoising flowgrams...\n"); + m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n"); + + while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){ + + if (m->control_pressed) { break; } + + double cycClock = clock(); + unsigned long long cycTime = time(NULL); + fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI); + + if (m->control_pressed) { break; } + + calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber); + + if (m->control_pressed) { break; } + + maxDelta = getNewWeights(numOTUs, cumNumSeqs, nSeqsPerOTU, singleTau, seqNumber, weight); + + if (m->control_pressed) { break; } + + double nLL = getLikelihood(numSeqs, numOTUs, nSeqsPerOTU, seqNumber, cumNumSeqs, seqIndex, dist, weight); + + if (m->control_pressed) { break; } + + checkCentroids(numOTUs, centroids, weight); + + if (m->control_pressed) { break; } + + calcNewDistances(numSeqs, numOTUs, nSeqsPerOTU, dist, weight, change, centroids, aaP, singleTau, aaI, seqNumber, seqIndex, uniqueFlowgrams, flowDataIntI, numFlowCells, lengths); + + if (m->control_pressed) { break; } + + iter++; + + m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n'); + + } + + if (m->control_pressed) { break; } + + m->mothurOut("\nFinalizing...\n"); + fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI); + + if (m->control_pressed) { break; } + + setOTUs(numOTUs, numSeqs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, otuData, singleTau, dist, aaP, aaI); + + if (m->control_pressed) { break; } + + vector otuCounts(numOTUs, 0); + for(int j=0;jcontrol_pressed) { break; } + + if ((large) && (g == 0)) { flowFileName = filenames[i]; theseFlowFileNames[0] = filenames[i]; } + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir = m->hasPath(flowFileName); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); + string qualityFileName = getOutputFileName("qfile",variables); + string fastaFileName = getOutputFileName("fasta",variables); + string nameFileName = getOutputFileName("name",variables); + string otuCountsFileName = getOutputFileName("counts",variables); + string fileRoot = m->getRootName(m->getSimpleName(flowFileName)); + int pos = fileRoot.find_first_of('.'); + string fileGroup = fileRoot; + if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); } + string groupFileName = getOutputFileName("group",variables); + + + writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; } + writeSequences(thisCompositeFASTAFileName, numOTUs, numFlowCells, fastaFileName, otuCounts, uniqueFlowgrams, seqNameVector, aaI, centroids);if (m->control_pressed) { break; } + writeNames(thisCompositeNamesFileName, numOTUs, nameFileName, otuCounts, seqNameVector, aaI, nSeqsPerOTU); if (m->control_pressed) { break; } + writeClusters(otuCountsFileName, numOTUs, numFlowCells,otuCounts, centroids, uniqueFlowgrams, seqNameVector, aaI, nSeqsPerOTU, lengths, flowDataIntI); if (m->control_pressed) { break; } + writeGroups(groupFileName, fileGroup, numSeqs, seqNameVector); if (m->control_pressed) { break; } + + if (large) { + if (g > 0) { + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])); + m->appendFiles(qualityFileName, getOutputFileName("qfile",variables)); + m->mothurRemove(qualityFileName); + m->appendFiles(fastaFileName, getOutputFileName("fasta",variables)); + m->mothurRemove(fastaFileName); + m->appendFiles(nameFileName, getOutputFileName("name",variables)); + m->mothurRemove(nameFileName); + m->appendFiles(otuCountsFileName, getOutputFileName("counts",variables)); + m->mothurRemove(otuCountsFileName); + m->appendFiles(groupFileName, getOutputFileName("group",variables)); + m->mothurRemove(groupFileName); + } + m->mothurRemove(theseFlowFileNames[g]); + } + } + + numCompleted++; + m->mothurOut("Total time to process " + fileNameForOutput + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n'); + } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + return numCompleted; + + }catch(exception& e) { + m->errorOut(e, "ShhherCommand", "driver"); + exit(1); + } +} + +/**************************************************************************************************/ +int ShhherCommand::getFlowData(string filename, vector& thisSeqNameVector, vector& thisLengths, vector& thisFlowDataIntI, map& thisNameMap, int& numFlowCells){ try{ - int minLength = lengths[mapSeqToUnique[seqA]]; - if(lengths[seqB] < minLength){ minLength = lengths[mapSeqToUnique[seqB]]; } + + ifstream flowFile; + + m->openInputFile(filename, flowFile); - int ANumFlowCells = seqA * numFlowCells; - int BNumFlowCells = seqB * numFlowCells; + string seqName; + int currentNumFlowCells; + float intensity; + thisSeqNameVector.clear(); + thisLengths.clear(); + thisFlowDataIntI.clear(); + thisNameMap.clear(); + + string numFlowTest; + flowFile >> numFlowTest; + + if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); } + else { convert(numFlowTest, numFlowCells); } + + if (m->debug) { m->mothurOut("[DEBUG]: numFlowCells = " + toString(numFlowCells) + ".\n"); } + int index = 0;//pcluster + while(!flowFile.eof()){ + + if (m->control_pressed) { break; } + + flowFile >> seqName >> currentNumFlowCells; + + thisLengths.push_back(currentNumFlowCells); + + thisSeqNameVector.push_back(seqName); + thisNameMap[seqName] = index++;//pcluster + + if (m->debug) { m->mothurOut("[DEBUG]: seqName = " + seqName + " length = " + toString(currentNumFlowCells) + " index = " + toString(index) + "\n"); } + + for(int i=0;i> intensity; + if(intensity > 9.99) { intensity = 9.99; } + int intI = int(100 * intensity + 0.0001); + thisFlowDataIntI.push_back(intI); + } + m->gobble(flowFile); + } + flowFile.close(); - float dist = 0; + int numSeqs = thisSeqNameVector.size(); - for(int i=0;icontrol_pressed) { break; } - int flowAIntI = flowDataIntI[ANumFlowCells + i]; - float flowAPrI = flowDataPrI[ANumFlowCells + i]; - - int flowBIntI = flowDataIntI[BNumFlowCells + i]; - float flowBPrI = flowDataPrI[BNumFlowCells + i]; - dist += jointLookUp[flowAIntI * NUMBINS + flowBIntI] - flowAPrI - flowBPrI; + int iNumFlowCells = i * numFlowCells; + for(int j=thisLengths[i];jerrorOut(e, "ShhherCommand", "calcPairwiseDist"); + m->errorOut(e, "ShhherCommand", "getFlowData"); exit(1); } } - /**************************************************************************************************/ -void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int stopSeq){ +int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int stopSeq, vector& mapUniqueToSeq, vector& mapSeqToUnique, vector& lengths, vector& flowDataPrI, vector& flowDataIntI){ try{ - + ostringstream outStream; outStream.setf(ios::fixed, ios::floatfield); outStream.setf(ios::dec, ios::basefield); @@ -1167,14 +2541,14 @@ void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int st int begTime = time(NULL); double begClock = clock(); - - for(int i=startSeq;icontrol_pressed) { break; } for(int j=0;jmothurOut(toString(i) + "\t" + toString(time(NULL) - begTime)); - m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)); - m->mothurOutEndLine(); + m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - begTime)); + m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n"); } } @@ -1195,139 +2568,128 @@ void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int st if (m->control_pressed) {} else { - m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime)); - m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)); - m->mothurOutEndLine(); + m->mothurOutJustToScreen(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime)); + m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n"); } + + return 0; } catch(exception& e) { m->errorOut(e, "ShhherCommand", "flowDistParentFork"); exit(1); } } - /**************************************************************************************************/ -string ShhherCommand::createDistFile(int processors){ +float ShhherCommand::calcPairwiseDist(int numFlowCells, int seqA, int seqB, vector& mapSeqToUnique, vector& lengths, vector& flowDataPrI, vector& flowDataIntI){ try{ -//////////////////////// until I figure out the shared memory issue ////////////////////// -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -#else - processors=1; -#endif -//////////////////////// until I figure out the shared memory issue ////////////////////// - - string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist"; - - unsigned long long begTime = time(NULL); - double begClock = clock(); + int minLength = lengths[mapSeqToUnique[seqA]]; + if(lengths[seqB] < minLength){ minLength = lengths[mapSeqToUnique[seqB]]; } - if (numSeqs < processors){ processors = 1; } + int ANumFlowCells = seqA * numFlowCells; + int BNumFlowCells = seqB * numFlowCells; - if(processors == 1) { flowDistParentFork(fDistFileName, 0, numUniques); } + float dist = 0; - else{ //you have multiple processors + for(int i=0;i start(processors, 0); - vector end(processors, 0); + if (m->control_pressed) { break; } - int process = 1; - vector processIDs; + int flowAIntI = flowDataIntI[ANumFlowCells + i]; + float flowAPrI = flowDataPrI[ANumFlowCells + i]; - for (int i = 0; i < processors; i++) { - start[i] = int(sqrt(float(i)/float(processors)) * numUniques); - end[i] = int(sqrt(float(i+1)/float(processors)) * numUniques); - } + int flowBIntI = flowDataIntI[BNumFlowCells + i]; + float flowBPrI = flowDataPrI[BNumFlowCells + i]; + dist += jointLookUp[flowAIntI * NUMBINS + flowBIntI] - flowAPrI - flowBPrI; + } + + dist /= (float) minLength; + return dist; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "calcPairwiseDist"); + exit(1); + } +} + +/**************************************************************************************************/ + +int ShhherCommand::getUniques(int numSeqs, int numFlowCells, vector& uniqueFlowgrams, vector& uniqueCount, vector& uniqueLengths, vector& mapSeqToUnique, vector& mapUniqueToSeq, vector& lengths, vector& flowDataPrI, vector& flowDataIntI){ + try{ + int numUniques = 0; + uniqueFlowgrams.assign(numFlowCells * numSeqs, -1); + uniqueCount.assign(numSeqs, 0); // anWeights + uniqueLengths.assign(numSeqs, 0); + mapSeqToUnique.assign(numSeqs, -1); + mapUniqueToSeq.assign(numSeqs, -1); + + vector uniqueFlowDataIntI(numFlowCells * numSeqs, -1); + + for(int i=0;i 0) { - processIDs.push_back(pid); //create map from line number to pid so you can append files in correct order later - process++; - }else if (pid == 0){ - flowDistParentFork(fDistFileName + toString(getpid()) + ".temp", start[process], end[process]); - exit(0); - }else { - m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine(); - perror(" : "); - for (int i=0;icontrol_pressed) { break; } - //parent does its part - flowDistParentFork(fDistFileName, start[0], end[0]); + int index = 0; - //force parent to wait until all the processes are done - for (int i=0;i pDataArray; - DWORD dwThreadIdArray[processors-1]; - HANDLE hThreadArray[processors-1]; - - //Create processor worker threads. - for(int i = 0; i < processors-1; i++){ - // Allocate memory for thread data. - string extension = extension = toString(i) + ".temp"; - - flowDistParentForkData* tempdist = new flowDistParentForkData((fDistFileName + extension), mapUniqueToSeq, mapSeqToUnique, lengths, flowDataIntI, flowDataPrI, jointLookUp, m, start[i+1], end[i+1], numFlowCells, cutoff, i); - pDataArray.push_back(tempdist); - processIDs.push_back(i); - - //MySeqSumThreadFunction is in header. It must be global or static to work with the threads. - //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier - hThreadArray[i] = CreateThread(NULL, 0, MyflowDistParentForkThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); + vector current(numFlowCells); + for(int j=0;j uniqueLengths[j]) { uniqueLengths[j] = lengths[i]; } + break; + } + index++; } -#endif - - //append and remove temp files - for (int i=0;iappendFiles((fDistFileName + toString(processIDs[i]) + ".temp"), fDistFileName); - m->mothurRemove((fDistFileName + toString(processIDs[i]) + ".temp")); + if(index == numUniques){ + uniqueLengths[numUniques] = lengths[i]; + uniqueCount[numUniques] = 1; + mapSeqToUnique[i] = numUniques;//anMap + mapUniqueToSeq[numUniques] = i;//anF + + for(int k=0;kmothurOutEndLine(); - m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n'); - - return fDistFileName; + flowDataPrI.resize(numSeqs * numFlowCells, 0); + for(int i=0;icontrol_pressed) { break; } flowDataPrI[i] = getProbIntensity(flowDataIntI[i]); } + + return numUniques; } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "createDistFile"); + m->errorOut(e, "ShhherCommand", "getUniques"); exit(1); } - } - /**************************************************************************************************/ - -string ShhherCommand::createNamesFile(){ +int ShhherCommand::createNamesFile(int numSeqs, int numUniques, string filename, vector& seqNameVector, vector& mapSeqToUnique, vector& mapUniqueToSeq){ try{ vector duplicateNames(numUniques, ""); @@ -1335,31 +2697,29 @@ string ShhherCommand::createNamesFile(){ duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ','; } - string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names"; - ofstream nameFile; - m->openOutputFile(nameFileName, nameFile); + m->openOutputFile(filename, nameFile); for(int i=0;icontrol_pressed) { break; } -// nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl; + // nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl; nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl; } nameFile.close(); - return nameFileName; + + return 0; } catch(exception& e) { m->errorOut(e, "ShhherCommand", "createNamesFile"); exit(1); } } - //********************************************************************************************************************** -string ShhherCommand::cluster(string distFileName, string namesFileName){ +int ShhherCommand::cluster(string filename, string distFileName, string namesFileName){ try { ReadMatrix* read = new ReadColumnMatrix(distFileName); @@ -1368,16 +2728,17 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){ NameAssignment* clusterNameMap = new NameAssignment(namesFileName); clusterNameMap->readMap(); read->read(clusterNameMap); - + ListVector* list = read->getListVector(); - SparseMatrix* matrix = read->getMatrix(); + SparseDistanceMatrix* matrix = read->getDMatrix(); delete read; delete clusterNameMap; - + RAbundVector* rabund = new RAbundVector(list->getRAbundVector()); - Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest"); + float adjust = -1.0; + Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest", adjust); string tag = cluster->getTag(); double clusterCutoff = cutoff; @@ -1390,33 +2751,41 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){ list->setLabel(toString(cutoff)); - string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.list"; ofstream listFile; - m->openOutputFile(listFileName, listFile); + m->openOutputFile(filename, listFile); list->print(listFile); listFile.close(); delete matrix; delete cluster; delete rabund; delete list; - - return listFileName; + + return 0; } catch(exception& e) { m->errorOut(e, "ShhherCommand", "cluster"); exit(1); } } - /**************************************************************************************************/ -void ShhherCommand::getOTUData(string listFileName){ +int ShhherCommand::getOTUData(int numSeqs, string fileName, vector& otuData, + vector& cumNumSeqs, + vector& nSeqsPerOTU, + vector >& aaP, //tMaster->aanP: each row is a different otu / each col contains the sequence indices + vector >& aaI, //tMaster->aanI: that are in each otu - can't differentiate between aaP and aaI + vector& seqNumber, //tMaster->anP: the sequence id number sorted by OTU + vector& seqIndex, + map& nameMap){ try { - + ifstream listFile; - m->openInputFile(listFileName, listFile); + m->openInputFile(fileName, listFile); string label; + int numOTUs; listFile >> label >> numOTUs; - + + if (m->debug) { m->mothurOut("[DEBUG]: Getting OTU Data...\n"); } + otuData.assign(numSeqs, 0); cumNumSeqs.assign(numOTUs, 0); nSeqsPerOTU.assign(numOTUs, 0); @@ -1431,11 +2800,12 @@ void ShhherCommand::getOTUData(string listFileName){ for(int i=0;icontrol_pressed) { break; } - + if (m->debug) { m->mothurOut("[DEBUG]: processing OTU " + toString(i) + ".\n"); } + listFile >> singleOTU; istringstream otuString(singleOTU); - + while(otuString){ string seqName = ""; @@ -1460,10 +2830,10 @@ void ShhherCommand::getOTUData(string listFileName){ } map::iterator nmIt = nameMap.find(seqName); - + int index = nmIt->second; nameMap.erase(nmIt); - + otuData[index] = i; nSeqsPerOTU[i]++; aaP[i].push_back(index); @@ -1489,6 +2859,8 @@ void ShhherCommand::getOTUData(string listFileName){ seqIndex = seqNumber; listFile.close(); + + return numOTUs; } catch(exception& e) { @@ -1496,125 +2868,28 @@ void ShhherCommand::getOTUData(string listFileName){ exit(1); } } - -/**************************************************************************************************/ - -void ShhherCommand::initPyroCluster(){ - try{ - - if (numOTUs < processors) { processors = 1; } - - dist.assign(numSeqs * numOTUs, 0); - change.assign(numOTUs, 1); - centroids.assign(numOTUs, -1); - weight.assign(numOTUs, 0); - singleTau.assign(numSeqs, 1.0); - - nSeqsBreaks.assign(processors+1, 0); - nOTUsBreaks.assign(processors+1, 0); - - nSeqsBreaks[0] = 0; - for(int i=0;ierrorOut(e, "ShhherCommand", "initPyroCluster"); - exit(1); - } -} - -/**************************************************************************************************/ - -void ShhherCommand::fill(){ - try { - int index = 0; - for(int i=0;icontrol_pressed) { break; } - - cumNumSeqs[i] = index; - for(int j=0;jerrorOut(e, "ShhherCommand", "fill"); - exit(1); - } -} - -/**************************************************************************************************/ - -void ShhherCommand::calcCentroids(){ - try{ - -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - - if(processors == 1) { - calcCentroidsDriver(0, numOTUs); - } - else{ //you have multiple processors - if (numOTUs < processors){ processors = 1; } - - int process = 1; - vector processIDs; - - //loop through and create all the processes you want - while (process != processors) { - int pid = vfork(); - - if (pid > 0) { - processIDs.push_back(pid); //create map from line number to pid so you can append files in correct order later - process++; - }else if (pid == 0){ - calcCentroidsDriver(nOTUsBreaks[process], nOTUsBreaks[process+1]); - exit(0); - }else { - m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine(); - perror(" : "); - for (int i=0;ierrorOut(e, "ShhherCommand", "calcCentroidsDriver"); - exit(1); - } -} - /**************************************************************************************************/ -void ShhherCommand::calcCentroidsDriver(int start, int finish){ +int ShhherCommand::calcCentroidsDriver(int numOTUs, + vector& cumNumSeqs, + vector& nSeqsPerOTU, + vector& seqIndex, + vector& change, //did the centroid sequence change? 0 = no; 1 = yes + vector& centroids, //the representative flowgram for each cluster m + vector& singleTau, //tMaster->adTau: 1-D Tau vector (1xnumSeqs) + vector& mapSeqToUnique, + vector& uniqueFlowgrams, + vector& flowDataIntI, + vector& lengths, + int numFlowCells, + vector& seqNumber){ //this function gets the most likely homopolymer length at a flow position for a group of sequences //within an otu try{ - for(int i=start;icontrol_pressed) { break; } @@ -1627,7 +2902,7 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){ for(int j=0;j 0 && count > MIN_COUNT){ vector adF(nSeqsPerOTU[i]); vector anL(nSeqsPerOTU[i]); @@ -1657,7 +2932,7 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){ double tauValue = singleTau[seqNumber[index]]; for(int k=0;kerrorOut(e, "ShhherCommand", "calcCentroidsDriver"); exit(1); } } - /**************************************************************************************************/ -double ShhherCommand::getDistToCentroid(int cent, int flow, int length){ +double ShhherCommand::getDistToCentroid(int cent, int flow, int length, vector& uniqueFlowgrams, + vector& flowDataIntI, int numFlowCells){ try{ int flowAValue = cent * numFlowCells; int flowBValue = flow * numFlowCells; double dist = 0; - + for(int i=0;i& cumNumSeqs, vector& nSeqsPerOTU, vector& singleTau, vector& seqNumber, vector& weight){ try{ double maxChange = 0; - for(int i=0;icontrol_pressed) { break; } - - double difference = weight[i]; - weight[i] = 0; - - for(int j=0;j maxChange){ maxChange = difference; } - } - return maxChange; - } - catch(exception& e) { - m->errorOut(e, "ShhherCommand", "getNewWeights"); - exit(1); - } -} - -/**************************************************************************************************/ - -double ShhherCommand::getLikelihood(){ - - try{ - - vector P(numSeqs, 0); - int effNumOTUs = 0; - - for(int i=0;i MIN_WEIGHT){ - effNumOTUs++; - } - } - - string hold; - for(int i=0;icontrol_pressed) { break; } - - for(int j=0;jerrorOut(e, "ShhherCommand", "getNewWeights"); - exit(1); - } -} - -/**************************************************************************************************/ - -void ShhherCommand::checkCentroids(){ - try{ - vector unique(numOTUs, 1); - - for(int i=0;icontrol_pressed) { break; } - - if(unique[i] == 1){ - for(int j=i+1;jerrorOut(e, "ShhherCommand", "checkCentroids"); - exit(1); - } -} - -/**************************************************************************************************/ - -void ShhherCommand::calcNewDistances(){ - try{ - -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - - if(processors == 1) { - calcNewDistancesParent(0, numSeqs); - } - else{ //you have multiple processors - if (numSeqs < processors){ processors = 1; } - - vector > child_otuIndex(processors); - vector > child_seqIndex(processors); - vector > child_singleTau(processors); - vector totals(processors); - - int process = 1; - vector processIDs; - - //loop through and create all the processes you want - while (process != processors) { - int pid = vfork(); - - if (pid > 0) { - processIDs.push_back(pid); //create map from line number to pid so you can append files in correct order later - process++; - }else if (pid == 0){ - calcNewDistancesChild(nSeqsBreaks[process], nSeqsBreaks[process+1], child_otuIndex[process], child_seqIndex[process], child_singleTau[process]); - totals[process] = child_otuIndex[process].size(); - - exit(0); - }else { - m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine(); - perror(" : "); - for (int i=0;ierrorOut(e, "ShhherCommand", "calcNewDistances"); - exit(1); - } -} - -/**************************************************************************************************/ -#ifdef USE_MPI -void ShhherCommand::calcNewDistancesChildMPI(int startSeq, int stopSeq, vector& otuIndex){ - - try{ - vector newTau(numOTUs,0); - vector norms(numSeqs, 0); - otuIndex.clear(); - seqIndex.clear(); - singleTau.clear(); - - for(int i=startSeq;icontrol_pressed) { break; } - - double offset = 1e8; - int indexOffset = i * numOTUs; - - for(int j=0;j MIN_WEIGHT && change[j] == 1){ - dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]); - } - if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){ - offset = dist[indexOffset + j]; - } - } - - for(int j=0;j MIN_WEIGHT){ - newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j]; - norms[i] += newTau[j]; - } - else{ - newTau[j] = 0.0; - } - } + for(int i=0;i MIN_TAU){ - otuIndex.push_back(j); - seqIndex.push_back(i); - singleTau.push_back(newTau[j]); - } + if (m->control_pressed) { break; } + + double difference = weight[i]; + weight[i] = 0; + + for(int j=0;j maxChange){ maxChange = difference; } } + return maxChange; } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "calcNewDistancesChildMPI"); + m->errorOut(e, "ShhherCommand", "getNewWeights"); exit(1); } } -#endif + /**************************************************************************************************/ -void ShhherCommand::calcNewDistancesChild(int startSeq, int stopSeq, vector& child_otuIndex, vector& child_seqIndex, vector& child_singleTau){ +double ShhherCommand::getLikelihood(int numSeqs, int numOTUs, vector& nSeqsPerOTU, vector& seqNumber, vector& cumNumSeqs, vector& seqIndex, vector& dist, vector& weight){ try{ - vector newTau(numOTUs,0); - vector norms(numSeqs, 0); - child_otuIndex.resize(0); - child_seqIndex.resize(0); - child_singleTau.resize(0); - for(int i=startSeq;i P(numSeqs, 0); + int effNumOTUs = 0; + + for(int i=0;i MIN_WEIGHT){ + effNumOTUs++; + } + } + + string hold; + for(int i=0;icontrol_pressed) { break; } - double offset = 1e8; - int indexOffset = i * numOTUs; - - - for(int j=0;j MIN_WEIGHT && change[j] == 1){ - dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]); - } + for(int j=0;j MIN_WEIGHT && dist[indexOffset + j] < offset){ - offset = dist[indexOffset + j]; - } + P[nI] += weight[i] * exp(-singleDist * sigma); } - - for(int j=0;j MIN_WEIGHT){ - newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j]; - norms[i] += newTau[j]; - } - else{ - newTau[j] = 0.0; - } + } + double nLL = 0.00; + for(int i=0;ierrorOut(e, "ShhherCommand", "getNewWeights"); + exit(1); + } +} + +/**************************************************************************************************/ + +int ShhherCommand::checkCentroids(int numOTUs, vector& centroids, vector& weight){ + try{ + vector unique(numOTUs, 1); + + for(int i=0;i MIN_TAU){ - child_otuIndex.push_back(j); - child_seqIndex.push_back(i); - child_singleTau.push_back(newTau[j]); + if (m->control_pressed) { break; } + + if(unique[i] == 1){ + for(int j=i+1;jerrorOut(e, "ShhherCommand", "calcNewDistancesChild"); + m->errorOut(e, "ShhherCommand", "checkCentroids"); exit(1); } } - /**************************************************************************************************/ -void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){ +void ShhherCommand::calcNewDistances(int numSeqs, int numOTUs, vector& nSeqsPerOTU, vector& dist, + vector& weight, vector& change, vector& centroids, + vector >& aaP, vector& singleTau, vector >& aaI, + vector& seqNumber, vector& seqIndex, + vector& uniqueFlowgrams, + vector& flowDataIntI, int numFlowCells, vector& lengths){ try{ @@ -2031,26 +3116,26 @@ void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){ vector newTau(numOTUs,0); vector norms(numSeqs, 0); nSeqsPerOTU.assign(numOTUs, 0); - - for(int i=startSeq;icontrol_pressed) { break; } int indexOffset = i * numOTUs; - + double offset = 1e8; for(int j=0;j MIN_WEIGHT && change[j] == 1){ - dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]); + dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i], uniqueFlowgrams, flowDataIntI, numFlowCells); } - + if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){ offset = dist[indexOffset + j]; } } - + for(int j=0;j MIN_WEIGHT){ newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j]; @@ -2060,11 +3145,11 @@ void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){ newTau[j] = 0.0; } } - + for(int j=0;j MIN_TAU){ @@ -2083,19 +3168,44 @@ void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){ nSeqsPerOTU[j]++; } } - + } - + } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "calcNewDistancesParent"); + m->errorOut(e, "ShhherCommand", "calcNewDistances"); exit(1); } } +/**************************************************************************************************/ +int ShhherCommand::fill(int numOTUs, vector& seqNumber, vector& seqIndex, vector& cumNumSeqs, vector& nSeqsPerOTU, vector >& aaP, vector >& aaI){ + try { + int index = 0; + for(int i=0;icontrol_pressed) { return 0; } + + cumNumSeqs[i] = index; + for(int j=0;jerrorOut(e, "ShhherCommand", "fill"); + exit(1); + } +} /**************************************************************************************************/ -void ShhherCommand::setOTUs(){ +void ShhherCommand::setOTUs(int numOTUs, int numSeqs, vector& seqNumber, vector& seqIndex, vector& cumNumSeqs, vector& nSeqsPerOTU, + vector& otuData, vector& singleTau, vector& dist, vector >& aaP, vector >& aaI){ try { vector bigTauMatrix(numOTUs * numSeqs, 0.0000); @@ -2138,24 +3248,25 @@ void ShhherCommand::setOTUs(){ nSeqsPerOTU[index]++; } - fill(); + + fill(numOTUs, seqNumber, seqIndex, cumNumSeqs, nSeqsPerOTU, aaP, aaI); } catch(exception& e) { - m->errorOut(e, "ShhherCommand", "calcNewDistances"); + m->errorOut(e, "ShhherCommand", "setOTUs"); exit(1); } } - /**************************************************************************************************/ -void ShhherCommand::writeQualities(vector otuCounts){ +void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string qualityFileName, vector otuCounts, vector& nSeqsPerOTU, vector& seqNumber, + vector& singleTau, vector& flowDataIntI, vector& uniqueFlowgrams, vector& cumNumSeqs, + vector& mapUniqueToSeq, vector& seqNameVector, vector& centroids, vector >& aaI){ try { - string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual"; - + ofstream qualityFile; m->openOutputFile(qualityFileName, qualityFile); - + qualityFile.setf(ios::fixed, ios::floatfield); qualityFile.setf(ios::showpoint); qualityFile << setprecision(6); @@ -2233,18 +3344,19 @@ void ShhherCommand::writeQualities(vector otuCounts){ if(otuCounts[i] > 0){ qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl; - + int j=4; //need to get past the first four bases while(qualities[i][j] != -1){ - qualityFile << qualities[i][j] << ' '; - j++; + qualityFile << qualities[i][j] << ' '; + if (j > qualities[i].size()) { break; } + j++; } qualityFile << endl; } } qualityFile.close(); - outputNames.push_back(qualityFileName); - + outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName); + } catch(exception& e) { m->errorOut(e, "ShhherCommand", "writeQualities"); @@ -2254,10 +3366,9 @@ void ShhherCommand::writeQualities(vector otuCounts){ /**************************************************************************************************/ -void ShhherCommand::writeSequences(vector otuCounts){ +void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTUs, int numFlowCells, string fastaFileName, vector otuCounts, vector& uniqueFlowgrams, vector& seqNameVector, vector >& aaI, vector& centroids){ try { - string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta"; ofstream fastaFile; m->openOutputFile(fastaFileName, fastaFile); @@ -2276,21 +3387,22 @@ void ShhherCommand::writeSequences(vector otuCounts){ for(int j=0;j= 4) { fastaFile << newSeq.substr(4) << endl; } + else { fastaFile << "NNNN" << endl; } } } fastaFile.close(); - - outputNames.push_back(fastaFileName); - - if(compositeFASTAFileName != ""){ - m->appendFiles(fastaFileName, compositeFASTAFileName); + + outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); + + if(thisCompositeFASTAFileName != ""){ + m->appendFiles(fastaFileName, thisCompositeFASTAFileName); } } catch(exception& e) { @@ -2301,9 +3413,9 @@ void ShhherCommand::writeSequences(vector otuCounts){ /**************************************************************************************************/ -void ShhherCommand::writeNames(vector otuCounts){ +void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, string nameFileName, vector otuCounts, vector& seqNameVector, vector >& aaI, vector& nSeqsPerOTU){ try { - string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names"; + ofstream nameFile; m->openOutputFile(nameFileName, nameFile); @@ -2322,11 +3434,11 @@ void ShhherCommand::writeNames(vector otuCounts){ } } nameFile.close(); - outputNames.push_back(nameFileName); + outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName); - if(compositeNamesFileName != ""){ - m->appendFiles(nameFileName, compositeNamesFileName); + if(thisCompositeNamesFileName != ""){ + m->appendFiles(nameFileName, thisCompositeNamesFileName); } } catch(exception& e) { @@ -2337,11 +3449,9 @@ void ShhherCommand::writeNames(vector otuCounts){ /**************************************************************************************************/ -void ShhherCommand::writeGroups(){ +void ShhherCommand::writeGroups(string groupFileName, string fileRoot, int numSeqs, vector& seqNameVector){ try { - string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.')); - string groupFileName = fileRoot + ".shhh.groups"; - ofstream groupFile; + ofstream groupFile; m->openOutputFile(groupFileName, groupFile); for(int i=0;ierrorOut(e, "ShhherCommand", "writeGroups"); @@ -2360,9 +3470,8 @@ void ShhherCommand::writeGroups(){ /**************************************************************************************************/ -void ShhherCommand::writeClusters(vector otuCounts){ +void ShhherCommand::writeClusters(string otuCountsFileName, int numOTUs, int numFlowCells, vector otuCounts, vector& centroids, vector& uniqueFlowgrams, vector& seqNameVector, vector >& aaI, vector& nSeqsPerOTU, vector& lengths, vector& flowDataIntI){ try { - string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts"; ofstream otuCountsFile; m->openOutputFile(otuCountsFileName, otuCountsFile); @@ -2379,7 +3488,7 @@ void ShhherCommand::writeClusters(vector otuCounts){ otuCountsFile << "ideal\t"; for(int j=8;j otuCounts){ string newSeq = ""; for(int k=0;k= 4) { otuCountsFile << newSeq.substr(4) << endl; } + else { otuCountsFile << "NNNN" << endl; } } otuCountsFile << endl; } } otuCountsFile.close(); - outputNames.push_back(otuCountsFileName); - + outputNames.push_back(otuCountsFileName); outputTypes["counts"].push_back(otuCountsFileName); + } catch(exception& e) { m->errorOut(e, "ShhherCommand", "writeClusters"); @@ -2416,4 +3527,92 @@ void ShhherCommand::writeClusters(vector otuCounts){ } } -//********************************************************************************************************************** +/**************************************************************************************************/ + +void ShhherCommand::getSingleLookUp(){ + try{ + // these are the -log probabilities that a signal corresponds to a particular homopolymer length + singleLookUp.assign(HOMOPS * NUMBINS, 0); + + int index = 0; + ifstream lookUpFile; + m->openInputFile(lookupFileName, lookUpFile); + + for(int i=0;icontrol_pressed) { break; } + + float logFracFreq; + lookUpFile >> logFracFreq; + + for(int j=0;j> singleLookUp[index]; + index++; + } + } + lookUpFile.close(); + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "getSingleLookUp"); + exit(1); + } +} + +/**************************************************************************************************/ + +void ShhherCommand::getJointLookUp(){ + try{ + + // the most likely joint probability (-log) that two intenities have the same polymer length + jointLookUp.resize(NUMBINS * NUMBINS, 0); + + for(int i=0;icontrol_pressed) { break; } + + for(int j=0;jerrorOut(e, "ShhherCommand", "getJointLookUp"); + exit(1); + } +} + +/**************************************************************************************************/ + +double ShhherCommand::getProbIntensity(int intIntensity){ + try{ + + double minNegLogProb = 100000000; + + + for(int i=0;icontrol_pressed) { break; } + + float negLogProb = singleLookUp[i * NUMBINS + intIntensity]; + if(negLogProb < minNegLogProb) { minNegLogProb = negLogProb; } + } + + return minNegLogProb; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "getProbIntensity"); + exit(1); + } +} + + + +