*/
#include "summaryqualcommand.h"
-
+#include "counttable.h"
//**********************************************************************************************************************
vector<string> 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<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
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";
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 {
//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
//check for required parameters
qualfile = validParameter.validFile(parameters, "qfile", true);
- if (qualfile == "not open") { abort = true; }
+ if (qualfile == "not open") { qualfile = ""; abort = true; }
else if (qualfile == "not found") {
qualfile = m->getQualFile();
if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
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"){
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
+
+
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(qualfile);
+ parser.getNameFile(files);
+ }
+ }
}
}
catch(exception& e) {
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<unsigned long long> positions;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(qualfile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
lines.push_back(linePair(0, 1000));
}else {
positions = m->setFilePosFasta(qualfile, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numSeqs / processors;
if (m->control_pressed) { return 0; }
//print summary file
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary";
+ map<string, string> 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; }
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();
if (current.getName() != "") {
int num = 1;
- if (namefile != "") {
+ if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(current.getName());
count += num;
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos.end)) { break; }
#else
int numSeqs = 0;
processIDS.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the seqSumQualData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
- //Taking advantage of shared memory to allow both threads to add info to vectors.
+ //Taking advantage of shared memory to pass results vectors.
//////////////////////////////////////////////////////////////////////////////////////////////////////
vector<seqSumQualData*> pDataArray;
DWORD dwThreadIdArray[processors];
HANDLE hThreadArray[processors];
+ bool hasNameMap = false;
+ if ((namefile !="") || (countfile != "")) { hasNameMap = true; }
+
//Create processor worker threads.
for( int i=0; i<processors; i++ ){
// Allocate memory for thread data.
- seqSumQualData* tempSum = new seqSumQualData(&position, &averageQ, &scores, filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+ seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, hasNameMap, nameMap);
pDataArray.push_back(tempSum);
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, MySeqSumQualThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}
//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); }
+ if (scores.size() < tempNum) {
+ scores.resize(tempNum);
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ for (int k = 0; k < tempNum; k++) { position[k] += pDataArray[i]->position[k]; }
+ for (int k = 0; k < tempNum; k++) { averageQ[k] += pDataArray[i]->averageQ[k]; }
+ for (int k = 0; k < tempNum; k++) { for (int j = 0; j < 41; j++) { scores[k][j] += pDataArray[i]->scores[k][j]; } }
+
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
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++) {
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