vector<string> TrimSeqsCommand::getValidParameters(){
try {
- string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
+ string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop","minlength", "maxlength", "qfile",
"qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
"keepfirst", "removelast",
"allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qual"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
else {
//valid paramters for this command
- string AlignArray[] = { "fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
+ string AlignArray[] = { "fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
"qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
"keepfirst", "removelast",
"allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qual"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
if (path == "") { parameters["qfile"] = inputDir + it->second; }
}
- it = parameters.find("group");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["group"] = inputDir + it->second; }
- }
}
else if(temp == "not open"){ abort = true; }
else { oligoFile = temp; }
- temp = validParameter.validFile(parameters, "group", true);
- if (temp == "not found"){ groupfile = ""; }
- else if(temp == "not open"){ abort = true; }
- else { groupfile = temp; }
temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
convert(temp, maxAmbig);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
- if ((oligoFile != "") && (groupfile != "")) {
- m->mothurOut("You given both a oligos file and a groupfile, only one is allowed."); m->mothurOutEndLine(); abort = true;
- }
-
- if(allFiles && (oligoFile == "") && (groupfile == "")){
- m->mothurOut("You selected allfiles, but didn't enter an oligos or group file. Ignoring the allfiles request."); m->mothurOutEndLine();
+ if(allFiles && (oligoFile == "")){
+ m->mothurOut("You selected allfiles, but didn't enter an oligos. Ignoring the allfiles request."); m->mothurOutEndLine();
}
if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
try {
m->mothurOut("The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n");
m->mothurOut("The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n");
- m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, group, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n");
+ m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n");
m->mothurOut("The fasta parameter is required.\n");
- m->mothurOut("The group parameter allows you to enter a group file for your fasta file.\n");
m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
m->mothurOut("The oligos parameter allows you to provide an oligos file.\n");
m->mothurOut("The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n");
if (qFileName != "") {
outputNames.push_back(trimQualFile);
outputNames.push_back(scrapQualFile);
- outputTypes["qual"].push_back(trimQualFile);
- outputTypes["qual"].push_back(scrapQualFile);
+ outputTypes["qfile"].push_back(trimQualFile);
+ outputTypes["qfile"].push_back(scrapQualFile);
}
string outputGroupFileName;
-
if(oligoFile != ""){
outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
- outputNames.push_back(outputGroupFileName); outputTypes["groups"].push_back(outputGroupFileName);
+ outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
getOligos(fastaFileNames, qualFileNames);
}
createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames);
}
#else
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
#endif
if (m->control_pressed) { return 0; }
-
if(allFiles){
+ //clear out all old group files
+ map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
+ map<string, string>::iterator it;
+ set<string> namesToRemove;
for(int i=0;i<fastaFileNames.size();i++){
for(int j=0;j<fastaFileNames[0].size();j++){
- if(m->isBlank(fastaFileNames[i][j])){
- remove(fastaFileNames[i][j].c_str());
-
- if(qFileName != ""){
+ if (fastaFileNames[i][j] != "") {
+ if(m->isBlank(fastaFileNames[i][j])){
remove(fastaFileNames[i][j].c_str());
+ namesToRemove.insert(fastaFileNames[i][j]);
+
+ if(qFileName != ""){
+ remove(qualFileNames[i][j].c_str());
+ namesToRemove.insert(qualFileNames[i][j]);
+ }
+ }else{
+ it = uniqueFastaNames.find(fastaFileNames[i][j]);
+ if (it == uniqueFastaNames.end()) {
+ uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
+ }
}
-
}
}
}
+
+ //remove names for outputFileNames, just cleans up the output
+ vector<string> outputNames2;
+ for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
+ outputNames = outputNames2;
+
+ for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
+ ifstream in;
+ m->openInputFile(it->first, in);
+
+ ofstream out;
+ string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + "groups";
+ outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
+ m->openOutputFile(thisGroupName, out);
+
+ while (!in.eof()){
+ if (m->control_pressed) { break; }
+
+ Sequence currSeq(in); m->gobble(in);
+ out << currSeq.getName() << '\t' << it->second << endl;
+ }
+ in.close();
+ out.close();
+ }
}
-
-
- if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //output group counts
+ m->mothurOutEndLine();
+ int total = 0;
+ for (int i = 0; i < barcodeNameVector.size(); i++) {
+ if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
}
+ if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
+
+ 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();
ofstream outGroupsFile;
if (oligoFile != ""){ m->openOutputFile(groupFileName, outGroupsFile); }
-
if(allFiles){
for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
- ofstream temp;
- m->openOutputFile(fastaFileNames[i][j], temp); temp.close();
- if(qFileName != ""){
- m->openOutputFile(qualFileNames[i][j], temp); temp.close();
+ if (fastaFileNames[i][j] != "") {
+ ofstream temp;
+ m->openOutputFile(fastaFileNames[i][j], temp); temp.close();
+ if(qFileName != ""){
+ m->openOutputFile(qualFileNames[i][j], temp); temp.close();
+ }
}
}
}
QualityScores currQual;
if(qFileName != ""){
- currQual = QualityScores(qFile, currSeq.getNumBases()); m->gobble(qFile);
+ currQual = QualityScores(qFile); m->gobble(qFile);
}
string origSeq = currSeq.getUnaligned();
if(barcodes.size() != 0){
outGroupsFile << currSeq.getName() << '\t' << barcodeNameVector[barcodeIndex] << endl;
+ groupCounts[barcodeIndex]++;
}
for(int i=0;i<tempFASTAFileNames.size();i++){
for(int j=0;j<tempFASTAFileNames[i].size();j++){
- tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
- m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
-
- if(qFileName != ""){
- tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
- m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
+ m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
+
+ if(qFileName != ""){
+ tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
+ m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
+ }
}
}
}
lines[process],
qLines[process]);
+ //pass groupCounts to parent
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ for(int i = 0; i < groupCounts.size(); i++) {
+ out << groupCounts[i] << endl;
+ }
+ out.close();
+
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
m->openOutputFile(trimQualFileName, temp); temp.close();
m->openOutputFile(scrapQualFileName, temp); temp.close();
-
-
driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
-
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
if(allFiles){
for(int j=0;j<fastaFileNames.size();j++){
for(int k=0;k<fastaFileNames[j].size();k++){
- m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
- remove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
-
- if(qFileName != ""){
- m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
- remove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ if (fastaFileNames[j][k] != "") {
+ m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
+ remove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+
+ if(qFileName != ""){
+ m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
+ remove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ }
}
}
}
}
+ ifstream in;
+ string tempFile = filename + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ int count = 0;
+ int tempNum;
+ while (!in.eof()) {
+ in >> tempNum; m->gobble(in);
+ groupCounts[count] += tempNum;
+ count++;
+ }
+ in.close(); remove(tempFile.c_str());
+
}
return exitCommand;
if(qFileName != ""){ qualFileNames = fastaFileNames; }
if(allFiles){
+ set<string> uniqueNames; //used to cleanup outputFileNames
for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
ofstream temp;
fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
- outputNames.push_back(fastaFileName);
- outputTypes["fasta"].push_back(fastaFileName);
+ if (uniqueNames.count(fastaFileName) == 0) {
+ outputNames.push_back(fastaFileName);
+ outputTypes["fasta"].push_back(fastaFileName);
+ uniqueNames.insert(fastaFileName);
+ }
+
fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
m->openOutputFile(fastaFileName, temp); temp.close();
if(qFileName != ""){
qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
- outputNames.push_back(qualFileName);
- outputTypes["qual"].push_back(qualFileName);
+ if (uniqueNames.count(fastaFileName) == 0) {
+ outputNames.push_back(qualFileName);
+ outputTypes["qfile"].push_back(qualFileName);
+ }
+
qualFileNames[itBar->second][itPrimer->second] = qualFileName;
m->openOutputFile(qualFileName, temp); temp.close();
}
}
numFPrimers = primers.size();
numRPrimers = revPrimer.size();
+ groupCounts.resize(barcodeNameVector.size(), 0);
}
catch(exception& e) {
projects / mothur.git / blobdiff