X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summaryqualcommand.cpp;h=e1e626ea273a650840dd849442e43762e9a100cf;hp=5c175106ecb2584d07ca15a06c71f27284a3571c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=91a27e0483827c06c21c4fe89558923bbfe86573 diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp index 5c17510..e1e626e 100644 --- a/summaryqualcommand.cpp +++ b/summaryqualcommand.cpp @@ -8,16 +8,17 @@ */ #include "summaryqualcommand.h" - +#include "counttable.h" //********************************************************************************************************************** vector SummaryQualCommand::setParameters(){ try { - CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pqual); + CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + 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); } @@ -32,9 +33,10 @@ vector SummaryQualCommand::setParameters(){ string SummaryQualCommand::getHelpString(){ try { string helpString = ""; - helpString += "The summary.qual command reads a quality file and an optional name file, and summarizes the quality information.\n"; - helpString += "The summary.tax command parameters are qfile, name and processors. qfile is required, unless you have a valid current quality file.\n"; + helpString += "The summary.qual command reads a quality file and an optional name or count file, and summarizes the quality information.\n"; + helpString += "The summary.tax command parameters are qfile, name, count and processors. qfile is required, unless you have a valid current quality file.\n"; helpString += "The name parameter allows you to enter a name file associated with your quality file. \n"; + helpString += "The count parameter allows you to enter a count file associated with your quality file. \n"; helpString += "The summary.qual command should be in the following format: \n"; helpString += "summary.qual(qfile=yourQualityFile) \n"; helpString += "Note: No spaces between parameter labels (i.e. qfile), '=' and parameters (i.e.yourQualityFile).\n"; @@ -45,7 +47,21 @@ string SummaryQualCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string SummaryQualCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "summary") { pattern = "[filename],qual.summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "SummaryQualCommand", "getOutputPattern"); + exit(1); + } +} //********************************************************************************************************************** SummaryQualCommand::SummaryQualCommand(){ try { @@ -103,6 +119,14 @@ SummaryQualCommand::SummaryQualCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } } //initialize outputTypes @@ -122,6 +146,13 @@ SummaryQualCommand::SummaryQualCommand(string option) { if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } //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"){ @@ -133,10 +164,13 @@ SummaryQualCommand::SummaryQualCommand(string option) { m->setProcessors(temp); m->mothurConvert(temp, processors); - if (namefile == "") { - vector files; files.push_back(qualfile); - parser.getNameFile(files); - } + + if (countfile == "") { + if (namefile == "") { + vector files; files.push_back(qualfile); + parser.getNameFile(files); + } + } } } catch(exception& e) { @@ -160,7 +194,12 @@ int SummaryQualCommand::execute(){ if (m->control_pressed) { return 0; } if (namefile != "") { nameMap = m->readNames(namefile); } - + else if (countfile != "") { + CountTable ct; + ct.readTable(countfile, false); + nameMap = ct.getNameMap(); + } + vector positions; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) positions = m->divideFile(qualfile, processors); @@ -189,7 +228,9 @@ int SummaryQualCommand::execute(){ if (m->control_pressed) { return 0; } //print summary file - string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile)); + string summaryFile = getOutputFileName("summary",variables); printQual(summaryFile, position, averageQ, scores); if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } @@ -207,7 +248,7 @@ int SummaryQualCommand::execute(){ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile); m->mothurOutEndLine(); @@ -238,7 +279,7 @@ int SummaryQualCommand::driverCreateSummary(vector& position, vector& if (current.getName() != "") { int num = 1; - if (namefile != "") { + if ((namefile != "") || (countfile != "")) { //make sure this sequence is in the namefile, else error map::iterator it = nameMap.find(current.getName()); @@ -381,11 +422,14 @@ int SummaryQualCommand::createProcessesCreateSummary(vector& position, vect DWORD dwThreadIdArray[processors]; HANDLE hThreadArray[processors]; + bool hasNameMap = false; + if ((namefile !="") || (countfile != "")) { hasNameMap = true; } + //Create processor worker threads. for( int i=0; i& position, vect //Close all thread handles and free memory allocations. for(int i=0; i < pDataArray.size(); i++){ - numSeqs += pDataArray[i]->count; + numSeqs += pDataArray[i]->numSeqs; + if (pDataArray[i]->count != pDataArray[i]->end) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; + } int tempNum = pDataArray[i]->position.size(); if (position.size() < tempNum) { position.resize(tempNum, 0); } if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); } @@ -438,7 +485,7 @@ int SummaryQualCommand::printQual(string sumFile, vector& position, vector< if (m->control_pressed) { out.close(); return 0; } - float average = averageQ[i] / (float) position[i]; + double average = averageQ[i] / (float) position[i]; out << i << '\t' << position[i] << '\t' << average << '\t'; for (int j = 0; j < 41; j++) {