//**********************************************************************************************************************
vector<string> FilterSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
- CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
- CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
- CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
- 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 pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
+ CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
+ CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
+ CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
+ CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
+ 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 FilterSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],filter.fasta"; }
+ else if (type == "filter") { pattern = "[filename],filter"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
FilterSeqsCommand::FilterSeqsCommand(){
try {
abort = true; calledHelp = true;
ofstream outFilter;
//prevent giantic file name
- string filterFile;
- if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
- else { filterFile = outputDir + filterFileName + ".filter"; }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + filterFileName + ".";
+ if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
+ string filterFile = getOutputFileName("filter", variables);
m->openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
+ string filteredFasta = getOutputFileName("fasta", variables);
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;
}
- if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
if(outputString != ""){ //output to file
delete buf;
}
- if((num) % 100 != 0){ cout << (num) << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+ if((num) % 100 != 0){ cout << (num) << endl; }
return 0;
}
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
out.close();
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ 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
//report progress
- if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
in.close();
return count;
cout.flush();
//report progress
- if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
//report progress
- if((num) % 100 != 0){ cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+ if((num) % 100 != 0){ cout << num << endl; }
return 0;
}
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ 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;
+ }
F.mergeFilter(pDataArray[i]->F.getFilter());
for (int k = 0; k < alignmentLength; k++) { F.a[k] += pDataArray[i]->F.a[k]; }