outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
getOligos(fastaFileNames, qualFileNames);
}
-
+ cout << fastaFileNames.size() << '\t' << qualFileNames.size() << endl;
vector<unsigned long int> fastaFilePos;
vector<unsigned long int> qFilePos;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
-
driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
-
- for (int j = 0; j < fastaFileNames.size(); j++) {
- rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
- }
- if(qFileName != ""){
- for (int j = 0; j < qualFileNames.size(); j++) {
- rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
- }
- }
-
}else{
createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
-
- 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());
-
- if(qFileName != ""){
- rename((trimQualFile + toString(processIDS[0]) + ".temp").c_str(), trimQualFile.c_str());
- rename((scrapQualFile + toString(processIDS[0]) + ".temp").c_str(), scrapQualFile.c_str());
- }
-
-
- for (int j = 0; j < fastaFileNames.size(); j++) {
- rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
- }
- if(qFileName != ""){
- for (int j = 0; j < qualFileNames.size(); j++) {
- rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
- }
- }
-
- //append files
- for(int i=1;i<processors;i++){
- m->appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
- remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
- m->appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
- remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
-
- m->appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
- remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
- m->appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
- remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
-
- m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
- remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
- for (int j = 0; j < fastaFileNames.size(); j++) {
- m->appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
- remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
- }
-
- if(qFileName != ""){
- for (int j = 0; j < qualFileNames.size(); j++) {
- m->appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
- remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
- }
- }
-
-
- }
- }
-
- if (m->control_pressed) { return 0; }
+ }
#else
driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
-
- for (int j = 0; j < fastaFileNames.size(); j++) {
- rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
- }
- if(qFileName != ""){
- for (int j = 0; j < qualFileNames.size(); j++) {
- rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
- }
- }
-
- if (m->control_pressed) { return 0; }
#endif
-
-
+
+ if (m->control_pressed) { return 0; }
+ cout << "done with driver " << endl;
for(int i=0;i<fastaFileNames.size();i++){
- if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
- else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
+ cout << fastaFileNames[i] << endl;
+
+ if (m->isBlank(fastaFileNames[i])) { cout << fastaFileNames[i] << " was blank" << endl; remove(fastaFileNames[i].c_str()); }
+ else if (filesToRemove.count(fastaFileNames[i]) > 0) { cout << fastaFileNames[i] << " was on the remove list" << endl; remove(fastaFileNames[i].c_str()); }
else {
ifstream inFASTA;
string seqName;
if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
}
}else{ thisGroup = groupVector[i]; }
-
+ cout << thisGroup << '\t' << i << '\t' << comboStarts << endl;
while(!inFASTA.eof()){
if(inFASTA.get() == '>'){
inFASTA >> seqName;
inFASTA.close();
}
}
-
+ cout << "done with fastaFileNames " << endl;
if(qFileName != ""){
for(int i=0;i<qualFileNames.size();i++){
- if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
- else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
+ cout << qualFileNames[i] << endl;
+ if (m->isBlank(qualFileNames[i])) { cout << qualFileNames[i] << " was blank" << endl; remove(qualFileNames[i].c_str()); }
+ else if (filesToRemove.count(qualFileNames[i]) > 0) { cout << qualFileNames[i] << " was on the remove list" << endl; remove(qualFileNames[i].c_str()); }
else {
ifstream inQual;
string seqName;
}
}
}
-
+ cout << "done with qualFileNames " << endl;
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
if (oligoFile != "") {
m->openOutputFile(groupFile, outGroups);
- for (int i = 0; i < fastaNames.size(); i++) {
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
- //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
- //clear old file if it exists
- ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- if(qFileName != ""){
- qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
- //qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
- //clear old file if it exists
- ofstream temp2;
- m->openOutputFile(qualNames[i], temp2);
- temp2.close();
- }
- #else
- //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
- fastaNames[i] = (fastaNames[i] + toString(i) + ".temp");
- ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- if(qFileName != ""){
- //qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));
- qualNames[i] = (qualNames[i] + toString(i) + ".temp");
- ofstream temp2;
- m->openOutputFile(qualNames[i], temp2);
- temp2.close();
- }
- #endif
- }
}
ifstream inFASTA;
if (m->control_pressed) {
inFASTA.close(); outFASTA.close(); scrapFASTA.close();
if (oligoFile != "") { outGroups.close(); }
-
- //for(int i=0;i<fastaFileNames.size();i++){ fastaFileNames[i]->close(); delete fastaFileNames[i]; }
if(qFileName != ""){
qFile.close();
- //for(int i=0;i<qualFileNames.size();i++){ qualFileNames[i]->close(); delete qualFileNames[i]; }
}
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
if (oligoFile != "") { outGroups.close(); }
if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); }
- //for(int i=0;i<fastaFileNames.size();i++){
- // fastaFileNames[i]->close();
- // delete fastaFileNames[i];
- //}
-
- //if(qFileName != ""){
- //for(int i=0;i<qualFileNames.size();i++){
- //qualFileNames[i]->close();
- //delete qualFileNames[i];
- //}
- //}
-
return count;
}
catch(exception& e) {
int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
+ int process = 1;
int exitCommand = 1;
processIDS.clear();
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){
+ for (int i = 0; i < fastaNames.size(); i++) {
+ fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
+ //clear old file if it exists
+ ofstream temp;
+ m->openOutputFile(fastaNames[i], temp);
+ temp.close();
+ if(qFileName != ""){
+ qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
+ //clear old file if it exists
+ ofstream temp2;
+ m->openOutputFile(qualNames[i], temp2);
+ temp2.close();
+ }
+ }
+
driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, lines[process], qLines[process]);
exit(0);
}else {
}
}
+ //parent do my part
+ for (int i = 0; i < fastaNames.size(); i++) {
+ //clear old file if it exists
+ ofstream temp;
+ m->openOutputFile(fastaNames[i], temp);
+ temp.close();
+ if(qFileName != ""){
+ //clear old file if it exists
+ ofstream temp2;
+ m->openOutputFile(qualNames[i], temp2);
+ temp2.close();
+ }
+ }
+
+ driverCreateTrim(filename, qFileName, trimFile, scrapFile, trimQFile, scrapQFile, groupFile, fastaNames, qualNames, lines[0], qLines[0]);
+
+
//force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
+ for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
+ //append files
+ for(int i=0;i<processIDS.size();i++){
+ m->mothurOut("Appending files from process " + processIDS[i]); m->mothurOutEndLine();
+
+ m->appendFiles((trimFile + toString(processIDS[i]) + ".temp"), trimFile);
+ remove((trimFile + toString(processIDS[i]) + ".temp").c_str());
+ m->appendFiles((scrapFile + toString(processIDS[i]) + ".temp"), scrapFile);
+ remove((scrapFile + toString(processIDS[i]) + ".temp").c_str());
+
+ m->mothurOut("Done with fasta files"); m->mothurOutEndLine();
+
+ if(qFileName != ""){
+ m->appendFiles((trimQFile + toString(processIDS[i]) + ".temp"), trimQFile);
+ remove((trimQFile + toString(processIDS[i]) + ".temp").c_str());
+ m->appendFiles((scrapQFile + toString(processIDS[i]) + ".temp"), scrapQFile);
+ remove((scrapQFile + toString(processIDS[i]) + ".temp").c_str());
+
+ m->mothurOut("Done with quality files"); m->mothurOutEndLine();
+ }
+
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+
+ m->mothurOut("Done with group file"); m->mothurOutEndLine();
+
+ for (int j = 0; j < fastaNames.size(); j++) {
+ m->appendFiles((fastaNames[j] + toString(processIDS[i]) + ".temp"), fastaNames[j]);
+ remove((fastaNames[j] + toString(processIDS[i]) + ".temp").c_str());
+ }
+
+ if(qFileName != ""){
+ for (int j = 0; j < qualNames.size(); j++) {
+ m->appendFiles((qualNames[j] + toString(processIDS[i]) + ".temp"), qualNames[j]);
+ remove((qualNames[j] + toString(processIDS[i]) + ".temp").c_str());
+ }
+ }
+
+ if (allFiles) { m->mothurOut("Done with allfile"); m->mothurOutEndLine(); }
+ }
+
return exitCommand;
#endif
}
projects / mothur.git / blobdiff