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 if (fastaFile == "not open") { abort = true; }
+ else { m->setFastaFile(fastaFile); }
//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"){
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligoFile = ""; }
else if(temp == "not open"){ abort = true; }
- else { oligoFile = temp; }
+ else { oligoFile = temp; m->setOligosFile(oligoFile); }
temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
temp = validParameter.validFile(parameters, "qfile", true);
if (temp == "not found") { qFileName = ""; }
else if(temp == "not open") { abort = true; }
- else { qFileName = temp; }
+ else { qFileName = temp; m->setQualFile(qFileName); }
temp = validParameter.validFile(parameters, "name", true);
if (temp == "not found") { nameFile = ""; }
- else if(temp == "not open") { abort = true; }
- else { nameFile = temp; }
+ else if(temp == "not open") { nameFile = ""; abort = true; }
+ else { nameFile = temp; m->setNameFile(nameFile); }
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
convert(temp, qThreshold);
//output group counts
m->mothurOutEndLine();
int total = 0;
+ if (groupCounts.size() != 0) { m->mothurOut("Group count: \n"); }
for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
- total += it->second; m->mothurOut("Group " + it->first + " contains " + toString(it->second) + " sequences."); m->mothurOutEndLine();
+ total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
}
if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
int currentSeqsDiffs = 0;
Sequence currSeq(inFASTA); m->gobble(inFASTA);
-
QualityScores currQual;
if(qFileName != ""){
currQual = QualityScores(qFile); m->gobble(qFile);
}
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
else { success = 1; }
-
+
//you don't want to trim, if it fails above then scrap it
if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+ if (nameFile != "") {
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ vector<string> thisSeqsNames;
+ m->splitAtChar(itName->second, thisSeqsNames, ',');
+ for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+ outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+ }
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+
map<string, int>::iterator it = groupCounts.find(thisGroup);
if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
else { groupCounts[it->first]++; }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
unsigned long int pos = inFASTA.tellg();
if ((pos == -1) || (pos >= line->end)) { break; }
+
#else
if (inFASTA.eof()) { break; }
#endif
-
+
//report progress
if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
}
//report progress
if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
+
inFASTA.close();
trimFASTAFile.close();
qLines[process]);
//pass groupCounts to parent
- ofstream out;
- string tempFile = filename + toString(getpid()) + ".num.temp";
- m->openOutputFile(tempFile, out);
- for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
- out << it->first << '\t' << it->second << endl;
+ if(oligoFile != ""){
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << groupCounts.size() << endl;
+
+ for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ }
+ out.close();
}
- out.close();
-
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
ofstream temp;
m->openOutputFile(trimFASTAFileName, temp); temp.close();
m->openOutputFile(scrapFASTAFileName, temp); temp.close();
- m->openOutputFile(trimQualFileName, temp); temp.close();
- m->openOutputFile(scrapQualFileName, temp); temp.close();
- m->openOutputFile(trimNameFileName, temp); temp.close();
- m->openOutputFile(scrapNameFileName, temp); temp.close();
+ if(qFileName != ""){
+ m->openOutputFile(trimQualFileName, temp); temp.close();
+ m->openOutputFile(scrapQualFileName, temp); temp.close();
+ }
+ if (nameFile != "") {
+ m->openOutputFile(trimNameFileName, temp); temp.close();
+ m->openOutputFile(scrapNameFileName, temp); temp.close();
+ }
driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
remove((scrapNameFileName + toString(processIDS[i]) + ".temp").c_str());
}
- m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
- remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+ if(oligoFile != ""){
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+ }
if(allFiles){
}
}
- ifstream in;
- string tempFile = filename + toString(processIDS[i]) + ".num.temp";
- m->openInputFile(tempFile, in);
- int tempNum;
- string group;
- while (!in.eof()) {
- in >> group >> tempNum; m->gobble(in);
+ if(oligoFile != ""){
+ ifstream in;
+ string tempFile = filename + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ int tempNum;
+ string group;
+
+ in >> tempNum; m->gobble(in);
+
+ if (tempNum != 0) {
+ while (!in.eof()) {
+ in >> group >> tempNum; m->gobble(in);
- map<string, int>::iterator it = groupCounts.find(group);
- if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
- else { groupCounts[it->first] += tempNum; }
+ map<string, int>::iterator it = groupCounts.find(group);
+ if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
+ else { groupCounts[it->first] += tempNum; }
+ }
+ }
+ in.close(); remove(tempFile.c_str());
}
- in.close(); remove(tempFile.c_str());
}
if (alignment != NULL) { delete alignment; }
}
-
+
return success;
}
projects / mothur.git / blobdiff