else {
//valid paramters for this command
string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
- "qthreshold", "qaverage", "allfiles", "qtrim", "outputdir","inputdir"};
+ "qthreshold", "qaverage", "allfiles", "qtrim", "processors", "outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
allFiles = isTrue(temp);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
if(allFiles && oligoFile == ""){
m->mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); m->mothurOutEndLine();
}
if (abort == true) { return 0; }
- vector<string> outputNames;
-
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
- ifstream inFASTA;
- openInputFile(fastaFile, inFASTA);
-
- ofstream outFASTA;
string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
- openOutputFile(trimSeqFile, outFASTA);
outputNames.push_back(trimSeqFile);
+ string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
+ outputNames.push_back(scrapSeqFile);
+ string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
- ofstream outGroups;
- vector<ofstream*> fastaFileNames;
+ vector<string> fastaFileNames;
if(oligoFile != ""){
- string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
- openOutputFile(groupFile, outGroups);
outputNames.push_back(groupFile);
getOligos(fastaFileNames);
}
+ if(qFileName != "") { setLines(qFileName, qLines); }
+
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastaFile, inFASTA);
+ int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+
+ for (int j = 0; j < fastaFileNames.size(); j++) {
+ rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
+ }
+
+ }else{
+ setLines(fastaFile, lines);
+ if(qFileName == "") { qLines = lines; }
+
+ createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames);
+
+ rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
+ rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
+ rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
+ for (int j = 0; j < fastaFileNames.size(); j++) {
+ rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
+ }
+ //append files
+ for(int i=1;i<processors;i++){
+ appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
+ remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
+ appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
+ remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
+ appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+ for (int j = 0; j < fastaFileNames.size(); j++) {
+ appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
+ remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
+ }
+ }
+ }
+
+ if (m->control_pressed) { return 0; }
+ #else
+ ifstream inFASTA;
+ openInputFile(fastafileNames[s], inFASTA);
+ numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+
+ if (m->control_pressed) { return 0; }
+ #endif
+
+
+ for(int i=0;i<fastaFileNames.size();i++){
+ ifstream inFASTA;
+ string seqName;
+ openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
+ ofstream outGroups;
+ openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
+ outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
+
+ while(!inFASTA.eof()){
+ if(inFASTA.get() == '>'){
+ inFASTA >> seqName;
+ outGroups << seqName << '\t' << groupVector[i] << endl;
+ }
+ while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+ }
+ outGroups.close();
+ inFASTA.close();
+ }
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ 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, "TrimSeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+/**************************************************************************************/
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, linePair* line, linePair* qline) {
+ try {
+
+ ofstream outFASTA;
+ int able = openOutputFile(trimFile, outFASTA);
+
ofstream scrapFASTA;
- string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
- openOutputFile(scrapSeqFile, scrapFASTA);
- outputNames.push_back(scrapSeqFile);
+ openOutputFile(scrapFile, scrapFASTA);
+
+ ofstream outGroups;
+ vector<ofstream*> fastaFileNames;
+ if (oligoFile != "") {
+ openOutputFile(groupFile, outGroups);
+ for (int i = 0; i < fastaNames.size(); i++) {
+ fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
+ }
+ }
+
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
ifstream qFile;
if(qFileName != "") { openInputFile(qFileName, qFile); }
- bool success;
-
- while(!inFASTA.eof()){
+ qFile.seekg(qline->start);
+ inFASTA.seekg(line->start);
+
+ for(int i=0;i<line->num;i++){
+
+ if (m->control_pressed) {
+ inFASTA.close();
+ outFASTA.close();
+ scrapFASTA.close();
+ if (oligoFile != "") { outGroups.close(); }
+ if(qFileName != "") { qFile.close(); }
+ for(int i=0;i<fastaFileNames.size();i++){
+ fastaFileNames[i]->close();
+ delete fastaFileNames[i];
+ }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ bool success = 1;
+
Sequence currSeq(inFASTA);
string origSeq = currSeq.getUnaligned();
}
gobble(inFASTA);
}
+
inFASTA.close();
outFASTA.close();
scrapFASTA.close();
- outGroups.close();
+ if (oligoFile != "") { outGroups.close(); }
if(qFileName != "") { qFile.close(); }
for(int i=0;i<fastaFileNames.size();i++){
delete fastaFileNames[i];
}
- for(int i=0;i<fastaFileNames.size();i++){
- string seqName;
- openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
- ofstream outGroups;
- openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
- outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ int exitCommand = 1;
+ processIDS.clear();
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
- while(!inFASTA.eof()){
- if(inFASTA.get() == '>'){
- inFASTA >> seqName;
- outGroups << seqName << '\t' << groupVector[i] << endl;
- }
- while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
- }
- outGroups.close();
- inFASTA.close();
+ 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){
+ driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- 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;
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ return exitCommand;
+#endif
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "execute");
+ m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
exit(1);
}
}
+/**************************************************************************************************/
+
+int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
+ try {
+
+ lines.clear();
+
+ vector<long int> positions;
+
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA);
+
+ if (input.length() != 0) {
+ if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ }
+ }
+ inFASTA.close();
+
+ int numFastaSeqs = positions.size();
+
+ FILE * pFile;
+ long size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ }else{
+ long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+ return numFastaSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "setLines");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
+void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
try {
ifstream inOligos;
openInputFile(oligoFile, inOligos);
groupVector.push_back(group);
if(allFiles){
- outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
+ //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
+ outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
}
}
}
bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
try {
string rawSequence = seq.getUnaligned();
- int seqLength = rawSequence.length();
- string name;
+ int seqLength; // = rawSequence.length();
+ string name, temp, temp2;
- qFile >> name;
+ qFile >> name >> temp;
+
+ splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
+ convert(temp, seqLength); //converts string to int
+
if (name.length() != 0) { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); } }
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
string name;
qFile >> name;
- if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
+ if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
projects / mothur.git / blobdiff