//**********************************************************************************************************************
vector<string> SeqSummaryCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- 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","summary",false,true,true); parameters.push_back(pfasta);
+ 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 SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SeqSummaryCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],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, "SeqSummaryCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
//set current fasta to fastafile
m->setFastaFile(fastafile);
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string summaryFile = getOutputFileName("summary",variables);
int numSeqs = 0;
if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, false);
nameMap = ct.getNameMap();
}
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
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();
}
#endif
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("summary");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
while (!done) {
if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
-
+
+ if (m->debug) { m->mothurOut("[DEBUG]: count = " + toString(count) + "\n"); }
+
Sequence current(in); m->gobble(in);
if (current.getName() != "") {
+ if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); }
+
int num = 1;
if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); }
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
if (in.eof()) { break; }
#endif
-
- //report progress
- //if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
}
- //report progress
- //if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
+
in.close();
return count;
//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;
+ }
for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) { startPosition.push_back(pDataArray[i]->startPosition[k]); }
for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) { endPosition.push_back(pDataArray[i]->endPosition[k]); }
for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]); }