#include "chopseqscommand.h"
#include "sequence.hpp"
+#include "removeseqscommand.h"
//**********************************************************************************************************************
-
+vector<string> ChopSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnumbases);
+ CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcountgaps);
+ CommandParameter pshort("short", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshort);
+ CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "","",false,false); parameters.push_back(pkeep);
+ 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); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChopSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n";
+ helpString += "The chop.seqs command parameters are fasta, name, group, count, numbases, countgaps and keep. fasta is required unless you have a valid current fasta file. numbases is required.\n";
+ helpString += "The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n";
+ helpString += "If you provide a name, group or count file any sequences removed from the fasta file will also be removed from those files.\n";
+ helpString += "The numbases parameter allows you to specify the number of bases you want to keep.\n";
+ helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
+ helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
+ helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+ helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
+ helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChopSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],chop.fasta"; }
+ else if (type == "name") { pattern = "[filename],chop.names"; }
+ else if (type == "group") { pattern = "[filename],chop.groups"; }
+ else if (type == "count") { pattern = "[filename],chop.count_table"; }
+ else if (type == "accnos") { pattern = "[filename],chop.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChopSeqsCommand::ChopSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","numbases","countgaps","keep","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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"){ outputDir = ""; }
-
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["count"] = 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);
if (inputDir == "not found"){ inputDir = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = 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; }
+ }
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") { //if there is a current fasta file, use it
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastafile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); 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"){ outputDir = ""; }
string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
- convert(temp, numbases);
+ m->mothurConvert(temp, numbases);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
temp = validParameter.validFile(parameters, "countgaps", false); if (temp == "not found") { temp = "f"; }
- countGaps = isTrue(temp);
+ countGaps = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "short", false); if (temp == "not found") { temp = "f"; }
+ Short = m->isTrue(temp);
keep = validParameter.validFile(parameters, "keep", false); if (keep == "not found") { keep = "front"; }
}
//**********************************************************************************************************************
-void ChopSeqsCommand::help(){
+int ChopSeqsCommand::execute(){
try {
- m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences.\n");
- m->mothurOut("The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta and numbases are required required.\n");
- m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n");
- m->mothurOut("The numbases parameter allows you to specify the number of bases you want to keep.\n");
- m->mothurOut("The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n");
- m->mothurOut("The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n");
- m->mothurOut("Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ map<string, string> variables;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("fasta", variables);
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
+ string outputFileNameAccnos = getOutputFileName("accnos", variables);
+
+ vector<unsigned long long> positions;
+ vector<linePair> lines;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ int numSeqs = 0;
+ positions = m->setFilePosFasta(fastafile, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+#endif
+
+ bool wroteAccnos = false;
+ if(processors == 1) { wroteAccnos = driver(lines[0], fastafile, outputFileName, outputFileNameAccnos); }
+ else { wroteAccnos = createProcesses(lines, fastafile, outputFileName, outputFileNameAccnos); }
+
+ if (m->control_pressed) { return 0; }
+
+ if (wroteAccnos) {
+ outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos);
+
+ //use remove.seqs to create new name, group and count file
+ if ((countfile != "") || (namefile != "") || (groupfile != "")) {
+ string inputString = "accnos=" + outputFileNameAccnos;
+
+ if (countfile != "") { inputString += ", count=" + countfile; }
+ else{
+ if (namefile != "") { inputString += ", name=" + namefile; }
+ if (groupfile != "") { inputString += ", group=" + groupfile; }
+ }
+
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: remove.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* removeCommand = new RemoveSeqsCommand(inputString);
+ removeCommand->execute();
+
+ map<string, vector<string> > filenames = removeCommand->getOutputFiles();
+
+ delete removeCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ if (groupfile != "") {
+ thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ string outGroup = getOutputFileName("group", variables);
+ m->renameFile(filenames["group"][0], outGroup);
+ outputNames.push_back(outGroup); outputTypes["group"].push_back(outGroup);
+ }
+
+ if (namefile != "") {
+ thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ string outName = getOutputFileName("name", variables);
+ m->renameFile(filenames["name"][0], outName);
+ outputNames.push_back(outName); outputTypes["name"].push_back(outName);
+ }
+
+ if (countfile != "") {
+ thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ string outCount = getOutputFileName("count", variables);
+ m->renameFile(filenames["count"][0], outCount);
+ outputNames.push_back(outCount); outputTypes["count"].push_back(outCount);
+ }
+ }
+ }
+ else { m->mothurRemove(outputFileNameAccnos); }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ if (wroteAccnos) { //set accnos file as new current accnosfile
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+ }
+
+ 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, "ChopSeqsCommand", "help");
+ m->errorOut(e, "ChopSeqsCommand", "execute");
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-int ChopSeqsCommand::execute(){
+/**************************************************************************************************/
+bool ChopSeqsCommand::createProcesses(vector<linePair> lines, string filename, string outFasta, string outAccnos) {
try {
+ int process = 1;
+ bool wroteAccnos = false;
+ vector<int> processIDS;
+ vector<string> nonBlankAccnosFiles;
+
+#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){
+ wroteAccnos = driver(lines[process], filename, outFasta + toString(getpid()) + ".temp", outAccnos + toString(getpid()) + ".temp");
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = fastafile + toString(getpid()) + ".bool.temp";
+ m->openOutputFile(tempFile, out);
+ out << wroteAccnos << 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);
+ }
+ }
- if (abort == true) { return 0; }
+ //do your part
+ wroteAccnos = driver(lines[0], filename, outFasta, outAccnos);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
- string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
- string outputFileNameAccnos = outputDir + getRootName(getSimpleName(fastafile)) + "chop.accnos";
+
+ if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
+ else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = fastafile + toString(processIDS[i]) + ".bool.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
+
+ bool temp;
+ in >> temp; m->gobble(in);
+ if (temp) { wroteAccnos = temp; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp"); }
+ else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp")); }
+
+ in.close();
+ m->mothurRemove(tempFilename);
+ }
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the seqSumData 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.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
- ofstream out;
- openOutputFile(outputFileName, out);
+ vector<chopData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
- ofstream outAcc;
- openOutputFile(outputFileNameAccnos, outAcc);
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+
+ string extension = "";
+ if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
+ // Allocate memory for thread data.
+ chopData* tempChop = new chopData(filename, (outFasta+extension), (outAccnos+extension), m, lines[i].start, lines[i].end, keep, countGaps, numbases, Short);
+ pDataArray.push_back(tempChop);
+
+ //MyChopThreadFunction 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, MyChopThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
- ifstream in;
- openInputFile(fastafile, in);
+ //do your part
+ wroteAccnos = driver(lines[processors-1], filename, (outFasta + toString(processors-1) + ".temp"), (outAccnos + toString(processors-1) + ".temp"));
+ processIDS.push_back(processors-1);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
- bool wroteAccnos = false;
+ if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
+ else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->wroteAccnos) { wroteAccnos = pDataArray[i]->wroteAccnos; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp"); }
+ else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp")); }
+ //check to make sure the process finished
+ 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;
+ }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ m->appendFiles((outFasta + toString(processIDS[i]) + ".temp"), outFasta);
+ m->mothurRemove((outFasta + toString(processIDS[i]) + ".temp"));
+ }
- while (!in.eof()) {
+ if (nonBlankAccnosFiles.size() != 0) {
+ m->renameFile(nonBlankAccnosFiles[0], outAccnos);
- Sequence seq(in);
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ m->appendFiles(nonBlankAccnosFiles[h], outAccnos);
+ m->mothurRemove(nonBlankAccnosFiles[h]);
+ }
+ }else { //recreate the accnosfile if needed
+ ofstream out;
+ m->openOutputFile(outAccnos, out);
+ out.close();
+ }
+
+ return wroteAccnos;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+bool ChopSeqsCommand::driver(linePair filePos, string filename, string outFasta, string outAccnos) {
+ try {
+
+ ofstream out;
+ m->openOutputFile(outFasta, out);
+
+ ofstream outAcc;
+ m->openOutputFile(outAccnos, outAcc);
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ in.seekg(filePos.start);
+
+ bool done = false;
+ bool wroteAccnos = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); out.close(); return 1; }
+
+ Sequence seq(in); m->gobble(in);
- if (m->control_pressed) { in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); outAcc.close(); m->mothurRemove(outFasta); m->mothurRemove(outAccnos); return 0; }
if (seq.getName() != "") {
string newSeqString = getChopped(seq);
outAcc << seq.getName() << endl;
wroteAccnos = true;
}
+ count++;
}
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos.end)) { break; }
+#else
+ if (in.eof()) { break; }
+#endif
+ //report progress
+ if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
}
- in.close();
- out.close();
- outAcc.close();
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
-
- if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); }
- else { remove(outputFileNameAccnos.c_str()); }
+ //report progress
+ if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
- m->mothurOutEndLine();
+ in.close();
+ out.close();
+ outAcc.close();
- return 0;
+ return wroteAccnos;
}
-
catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "execute");
+ m->errorOut(e, "ChopSeqsCommand", "driver");
exit(1);
}
}
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+ if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
numBasesCounted++;
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot); }
+ else { temp = temp.substr(0, stopSpot+1); }
- }else { temp = ""; } //sequence too short
-
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
}else { //you are keeping the back
int tempLength = temp.length();
if (tempLength > numbases) { //you have enough bases to remove some
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
- if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+ if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
numBasesCounted++;
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(stopSpot+1); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
}
- else { temp = ""; } //sequence too short
}
}else{
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
+ temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(0, stopSpot); }
+ else { temp = temp.substr(0, stopSpot+1); }
- }else { temp = ""; } //sequence too short
-
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
+ }
}else { //you are keeping the back
int tempLength = tempUnaligned.length();
if (tempLength > numbases) { //you have enough bases to remove some
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
- temp[i] == '.';
+ temp[i] = '.';
tempLength--;
if (tempLength < numbases) { stopSpot = 0; break; }
}
}
if (stopSpot == 0) { temp = ""; }
- else { temp = temp.substr(stopSpot+1); }
+ else { temp = temp.substr(stopSpot); }
+ }else {
+ if (!Short) { temp = ""; } //sequence too short
}
- else { temp = ""; } //sequence too short
}
}
projects / mothur.git / blobdiff