//**********************************************************************************************************************
vector<string> ChimeraUchimeCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- 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-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- 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 pabskew("abskew", "Number", "", "1.9", "", "", "",false,false); parameters.push_back(pabskew);
- CommandParameter pchimealns("chimealns", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pchimealns);
- CommandParameter pminh("minh", "Number", "", "0.3", "", "", "",false,false); parameters.push_back(pminh);
- CommandParameter pmindiv("mindiv", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pmindiv);
- CommandParameter pxn("xn", "Number", "", "8.0", "", "", "",false,false); parameters.push_back(pxn);
- CommandParameter pdn("dn", "Number", "", "1.4", "", "", "",false,false); parameters.push_back(pdn);
- CommandParameter pxa("xa", "Number", "", "1", "", "", "",false,false); parameters.push_back(pxa);
- CommandParameter pchunks("chunks", "Number", "", "4", "", "", "",false,false); parameters.push_back(pchunks);
- CommandParameter pminchunk("minchunk", "Number", "", "64", "", "", "",false,false); parameters.push_back(pminchunk);
- CommandParameter pidsmoothwindow("idsmoothwindow", "Number", "", "32", "", "", "",false,false); parameters.push_back(pidsmoothwindow);
- CommandParameter pdups("dereplicate", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdups);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",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-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pstrand("strand", "String", "", "", "", "", "","",false,false); parameters.push_back(pstrand);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter pabskew("abskew", "Number", "", "1.9", "", "", "","",false,false); parameters.push_back(pabskew);
+ CommandParameter pchimealns("chimealns", "Boolean", "", "F", "", "", "","alns",false,false); parameters.push_back(pchimealns);
+ CommandParameter pminh("minh", "Number", "", "0.3", "", "", "","",false,false); parameters.push_back(pminh);
+ CommandParameter pmindiv("mindiv", "Number", "", "0.5", "", "", "","",false,false); parameters.push_back(pmindiv);
+ CommandParameter pxn("xn", "Number", "", "8.0", "", "", "","",false,false); parameters.push_back(pxn);
+ CommandParameter pdn("dn", "Number", "", "1.4", "", "", "","",false,false); parameters.push_back(pdn);
+ CommandParameter pxa("xa", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pxa);
+ CommandParameter pchunks("chunks", "Number", "", "4", "", "", "","",false,false); parameters.push_back(pchunks);
+ CommandParameter pminchunk("minchunk", "Number", "", "64", "", "", "","",false,false); parameters.push_back(pminchunk);
+ CommandParameter pidsmoothwindow("idsmoothwindow", "Number", "", "32", "", "", "","",false,false); parameters.push_back(pidsmoothwindow);
+ CommandParameter pdups("dereplicate", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdups);
//CommandParameter pminsmoothid("minsmoothid", "Number", "", "0.95", "", "", "",false,false); parameters.push_back(pminsmoothid);
- CommandParameter pmaxp("maxp", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxp);
- CommandParameter pskipgaps("skipgaps", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps);
- CommandParameter pskipgaps2("skipgaps2", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps2);
- CommandParameter pminlen("minlen", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminlen);
- CommandParameter pmaxlen("maxlen", "Number", "", "10000", "", "", "",false,false); parameters.push_back(pmaxlen);
- CommandParameter pucl("ucl", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pucl);
- CommandParameter pqueryfract("queryfract", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pqueryfract);
+ CommandParameter pmaxp("maxp", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmaxp);
+ CommandParameter pskipgaps("skipgaps", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pskipgaps);
+ CommandParameter pskipgaps2("skipgaps2", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pskipgaps2);
+ CommandParameter pminlen("minlen", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pminlen);
+ CommandParameter pmaxlen("maxlen", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(pmaxlen);
+ CommandParameter pucl("ucl", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pucl);
+ CommandParameter pqueryfract("queryfract", "Number", "", "0.5", "", "", "","",false,false); parameters.push_back(pqueryfract);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string helpString = "";
helpString += "The chimera.uchime command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
helpString += "This command is a wrapper for uchime written by Robert C. Edgar.\n";
- helpString += "The chimera.uchime command parameters are fasta, name, count, reference, processors, dereplicate, abskew, chimealns, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, skipgaps, skipgaps2, minlen, maxlen, ucl and queryfact.\n";
+ helpString += "The chimera.uchime command parameters are fasta, name, count, reference, processors, dereplicate, abskew, chimealns, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, skipgaps, skipgaps2, minlen, maxlen, ucl, strand and queryfact.\n";
helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
- helpString += "The count parameter allows you to provide a count file, if you are using template=self. \n";
+ helpString += "The count parameter allows you to provide a count file, if you are using template=self. When you use a count file with group info and dereplicate=T, mothur will create a *.pick.count_table file containing seqeunces after chimeras are removed. \n";
helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
helpString += "The group parameter allows you to provide a group file. The group file can be used with a namesfile and reference=self. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
helpString += "If the dereplicate parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric, default=f.\n";
}
}
//**********************************************************************************************************************
-string ChimeraUchimeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraUchimeCommand::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 == "chimera") { outputFileName = "uchime.chimeras"; }
- else if (type == "accnos") { outputFileName = "uchime.accnos"; }
- else if (type == "alns") { outputFileName = "uchime.alns"; }
- 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, "ChimeraUchimeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],uchime.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],uchime.accnos"; }
+ else if (type == "alns") { pattern = "[filename],uchime.alns"; }
+ else if (type == "count") { pattern = "[filename],uchime.pick.count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraUchimeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraUchimeCommand::ChimeraUchimeCommand(){
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["alns"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "ChimeraUchimeCommand", "ChimeraUchimeCommand");
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["alns"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
maxp = validParameter.validFile(parameters, "maxp", false); if (maxp == "not found") { useMaxp = false; maxp = "2"; } else{ useMaxp = true; }
minlen = validParameter.validFile(parameters, "minlen", false); if (minlen == "not found") { useMinlen = false; minlen = "10"; } else{ useMinlen = true; }
maxlen = validParameter.validFile(parameters, "maxlen", false); if (maxlen == "not found") { useMaxlen = false; maxlen = "10000"; } else{ useMaxlen = true; }
+
+ strand = validParameter.validFile(parameters, "strand", false); if (strand == "not found") { strand = ""; }
temp = validParameter.validFile(parameters, "ucl", false); if (temp == "not found") { temp = "f"; }
ucl = m->isTrue(temp);
temp = validParameter.validFile(parameters, "skipgaps2", false); if (temp == "not found") { temp = "t"; }
skipgaps2 = m->isTrue(temp);
- string usedDups = "false";
+
temp = validParameter.validFile(parameters, "dereplicate", false);
- if (temp == "not found") {
- if (groupfile != "") { temp = "false"; }
- else { temp = "true"; usedDups = ""; }
- }
+ if (temp == "not found") { temp = "false"; }
dups = m->isTrue(temp);
if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+ if (hasCount && (templatefile != "self")) { m->mothurOut("You have provided a countfile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
//look for uchime exe
int start = time(NULL);
string nameFile = "";
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
- string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("alns");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string outputFileName = getOutputFileName("chimera", variables);
+ string accnosFileName = getOutputFileName("accnos", variables);
+ string alnsFileName = getOutputFileName("alns", variables);
string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
+ string newCountFile = "";
//you provided a groupfile
string groupFile = "";
else if (hasCount) {
CountTable ct;
if (ct.testGroups(nameFileNames[s])) { hasGroup = true; }
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFileNames[s]));
+ newCountFile = getOutputFileName("count", variables);
}
if ((templatefile == "self") && (!hasGroup)) { //you want to run uchime with a template=self and no groups
int error;
if (hasCount) {
CountTable ct;
- ct.readTable(nameFile);
+ ct.readTable(nameFile, true, false);
for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
int num = ct.getNumSeqs(it->first);
if (num == 0) { error = 1; }
if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); }
int totalSeqs = 0;
- if(processors == 1) { totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); }
- else { totalSeqs = createProcessesGroups(outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]); }
+ if(processors == 1) { totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
+
+ if (hasCount && dups) {
+ CountTable c; c.readTable(nameFile, true, false);
+ if (!m->isBlank(newCountFile)) {
+ ifstream in2;
+ m->openInputFile(newCountFile, in2);
+
+ string name, group;
+ while (!in2.eof()) {
+ in2 >> name >> group; m->gobble(in2);
+ c.setAbund(name, group, 0);
+ }
+ in2.close();
+ }
+ m->mothurRemove(newCountFile);
+ c.printTable(newCountFile);
+ }
+
+ }else { totalSeqs = createProcessesGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, groups, nameFile, groupFile, fastaFileNames[s]); }
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
- if (hasCount) { delete cparser; }
- else { delete sparser; }
+
if (!dups) {
int totalChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName, alnsFileName);
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(totalSeqs) + " sequences. " + toString(totalChimeras) + " chimeras were found."); m->mothurOutEndLine();
m->mothurOut("The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples."); m->mothurOutEndLine();
- }
+ }else {
+
+ if (hasCount) {
+ set<string> doNotRemove;
+ CountTable c; c.readTable(newCountFile, true, true);
+ vector<string> namesInTable = c.getNamesOfSeqs();
+ for (int i = 0; i < namesInTable.size(); i++) {
+ int temp = c.getNumSeqs(namesInTable[i]);
+ if (temp == 0) { c.remove(namesInTable[i]); }
+ else { doNotRemove.insert((namesInTable[i])); }
+ }
+ //remove names we want to keep from accnos file.
+ set<string> accnosNames = m->readAccnos(accnosFileName);
+ ofstream out2;
+ m->openOutputFile(accnosFileName, out2);
+ for (set<string>::iterator it = accnosNames.begin(); it != accnosNames.end(); it++) {
+ if (doNotRemove.count(*it) == 0) { out2 << (*it) << endl; }
+ }
+ out2.close();
+ c.printTable(newCountFile);
+ outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
+ }
+ }
+
+ if (hasCount) { delete cparser; }
+ else { delete sparser; }
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
}
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
map<string, string>::iterator itUnique;
int total = 0;
- //edit accnos file
- ifstream in2;
- m->openInputFile(accnosFileName, in2);
-
ofstream out2;
m->openOutputFile(accnosFileName+".temp", out2);
set<string> chimerasInFile;
set<string>::iterator itChimeras;
-
- while (!in2.eof()) {
- if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
-
- in2 >> name; m->gobble(in2);
-
- //find unique name
- itUnique = uniqueNames.find(name);
-
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- itChimeras = chimerasInFile.find((itUnique->second));
-
- if (itChimeras == chimerasInFile.end()) {
- out2 << itUnique->second << endl;
- chimerasInFile.insert((itUnique->second));
- total++;
- }
- }
- }
- in2.close();
+ if (!m->isBlank(accnosFileName)) {
+ //edit accnos file
+ ifstream in2;
+ m->openInputFile(accnosFileName, in2);
+
+ while (!in2.eof()) {
+ if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+
+ in2 >> name; m->gobble(in2);
+
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ itChimeras = chimerasInFile.find((itUnique->second));
+
+ if (itChimeras == chimerasInFile.end()) {
+ out2 << itUnique->second << endl;
+ chimerasInFile.insert((itUnique->second));
+ total++;
+ }
+ }
+ }
+ in2.close();
+ }
out2.close();
m->mothurRemove(accnosFileName);
}
}
//**********************************************************************************************************************
-int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, string accnos, string alns, int start, int end, vector<string> groups){
+int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, string accnos, string alns, string countlist, int start, int end, vector<string> groups){
try {
int totalSeqs = 0;
int numChimeras = 0;
-
+
+
+ ofstream outCountList;
+ if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }
+
for (int i = start; i < end; i++) {
- int start = time(NULL); if (m->control_pressed) { return 0; }
+ int start = time(NULL); if (m->control_pressed) { outCountList.close(); m->mothurRemove(countlist); return 0; }
int error;
if (hasCount) { error = cparser->getSeqs(groups[i], filename, true); if ((error == 1) || m->control_pressed) { return 0; } }
else { error = sparser->getSeqs(groups[i], filename, true); if ((error == 1) || m->control_pressed) { return 0; } }
- int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
+ int numSeqs = driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
totalSeqs += numSeqs;
if (m->control_pressed) { return 0; }
if (!m->debug) { m->mothurRemove(filename); }
else { m->mothurOut("[DEBUG]: saving file: " + filename + ".\n"); }
+ //if we provided a count file with group info and set dereplicate=t, then we want to create a *.pick.count_table
+ //This table will zero out group counts for seqs determined to be chimeric by that group.
+ if (dups) {
+ if (!m->isBlank(accnos+groups[i])) {
+ ifstream in;
+ m->openInputFile(accnos+groups[i], in);
+ string name;
+ if (hasCount) {
+ while (!in.eof()) {
+ in >> name; m->gobble(in);
+ outCountList << name << '\t' << groups[i] << endl;
+ }
+ in.close();
+ }else {
+ map<string, string> thisnamemap = sparser->getNameMap(groups[i]);
+ map<string, string>::iterator itN;
+ ofstream out;
+ m->openOutputFile(accnos+groups[i]+".temp", out);
+ while (!in.eof()) {
+ in >> name; m->gobble(in);
+ itN = thisnamemap.find(name);
+ if (itN != thisnamemap.end()) {
+ vector<string> tempNames; m->splitAtComma(itN->second, tempNames);
+ for (int j = 0; j < tempNames.size(); j++) { out << tempNames[j] << endl; }
+
+ }else { m->mothurOut("[ERROR]: parsing cannot find " + name + ".\n"); m->control_pressed = true; }
+ }
+ out.close();
+ in.close();
+ m->renameFile(accnos+groups[i]+".temp", accnos+groups[i]);
+ }
+
+ }
+ }
+
//append files
m->appendFiles((outputFName+groups[i]), outputFName); m->mothurRemove((outputFName+groups[i]));
m->appendFiles((accnos+groups[i]), accnos); m->mothurRemove((accnos+groups[i]));
if (chimealns) { m->appendFiles((alns+groups[i]), alns); m->mothurRemove((alns+groups[i])); }
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + groups[i] + "."); m->mothurOutEndLine();
- }
- return totalSeqs;
+ }
+
+ if (hasCount && dups) { outCountList.close(); }
+
+ return totalSeqs;
}
catch(exception& e) {
*tempa = '\0'; strncat(tempa, alns.c_str(), alns.length());
cPara.push_back(tempa);
}
+
+ if (strand != "") {
+ char* tempA = new char[9];
+ *tempA = '\0'; strncat(tempA, "--strand", 8);
+ cPara.push_back(tempA);
+ char* tempa = new char[strand.length()+1];
+ *tempa = '\0'; strncat(tempa, strand.c_str(), strand.length());
+ cPara.push_back(tempa);
+ }
if (useAbskew) {
char* tempskew = new char[9];
// Allocate memory for thread data.
string extension = toString(i) + ".temp";
- uchimeData* tempUchime = new uchimeData(outputFileName+extension, uchimeLocation, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0, i);
- tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
- tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+ uchimeData* tempUchime = new uchimeData(outputFileName+extension, uchimeLocation, templatefile, files[i], "", "", "", accnos+extension, alns+extension, "", dummy, m, 0, 0, i);
+ tempUchime->setBooleans(dups, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
+ tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, strand);
pDataArray.push_back(tempUchime);
processIDS.push_back(i);
}
/**************************************************************************************************/
-int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filename, string accnos, string alns, vector<string> groups, string nameFile, string groupFile, string fastaFile) {
+int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filename, string accnos, string alns, string newCountFile, vector<string> groups, string nameFile, string groupFile, string fastaFile) {
try {
processIDS.clear();
int process = 1;
int num = 0;
+
+ CountTable newCount;
+ if (hasCount && dups) { newCount.readTable(nameFile, true, false); }
//sanity check
if (groups.size() < processors) { processors = groups.size(); }
//divide the groups between the processors
vector<linePair> lines;
- int numGroupsPerProcessor = groups.size() / processors;
- for (int i = 0; i < processors; i++) {
- int startIndex = i * numGroupsPerProcessor;
- int endIndex = (i+1) * numGroupsPerProcessor;
- if(i == (processors - 1)){ endIndex = groups.size(); }
- lines.push_back(linePair(startIndex, endIndex));
- }
-
+ int remainingPairs = groups.size();
+ int startIndex = 0;
+ for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
+ int numPairs = remainingPairs; //case for last processor
+ if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
+ lines.push_back(linePair(startIndex, (startIndex+numPairs))); //startIndex, endIndex
+ startIndex = startIndex + numPairs;
+ remainingPairs = remainingPairs - numPairs;
+ }
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
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){
- num = driverGroups(outputFName + toString(getpid()) + ".temp", filename + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", alns + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+ num = driverGroups(outputFName + toString(getpid()) + ".temp", filename + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", alns + toString(getpid()) + ".temp", accnos + ".byCount." + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
//pass numSeqs to parent
ofstream out;
}
//do my part
- num = driverGroups(outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
+ num = driverGroups(outputFName, filename, accnos, alns, accnos + ".byCount", lines[0].start, lines[0].end, groups);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
-
+
for (int i = 0; i < processIDS.size(); i++) {
ifstream in;
string tempFile = outputFName + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); m->mothurRemove(tempFile);
- }
-
+ }
+
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the uchimeData struct.
// Allocate memory for thread data.
string extension = toString(i) + ".temp";
- uchimeData* tempUchime = new uchimeData(outputFName+extension, uchimeLocation, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end, i);
- tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
- tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+ uchimeData* tempUchime = new uchimeData(outputFName+extension, uchimeLocation, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, accnos+".byCount."+extension, groups, m, lines[i].start, lines[i].end, i);
+ tempUchime->setBooleans(dups, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
+ tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, strand);
pDataArray.push_back(tempUchime);
processIDS.push_back(i);
//using the main process as a worker saves time and memory
- num = driverGroups(outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
+ num = driverGroups(outputFName, filename, accnos, alns, accnos + ".byCount", lines[0].start, lines[0].end, groups);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
+
+
#endif
-
-
+
+ //read my own
+ if (hasCount && dups) {
+ if (!m->isBlank(accnos + ".byCount")) {
+ ifstream in2;
+ m->openInputFile(accnos + ".byCount", in2);
+
+ string name, group;
+ while (!in2.eof()) {
+ in2 >> name >> group; m->gobble(in2);
+ newCount.setAbund(name, group, 0);
+ }
+ in2.close();
+ }
+ m->mothurRemove(accnos + ".byCount");
+ }
+
//append output files
for(int i=0;i<processIDS.size();i++){
m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
m->appendFiles((alns + toString(processIDS[i]) + ".temp"), alns);
m->mothurRemove((alns + toString(processIDS[i]) + ".temp"));
}
+
+ if (hasCount && dups) {
+ if (!m->isBlank(accnos + ".byCount." + toString(processIDS[i]) + ".temp")) {
+ ifstream in2;
+ m->openInputFile(accnos + ".byCount." + toString(processIDS[i]) + ".temp", in2);
+
+ string name, group;
+ while (!in2.eof()) {
+ in2 >> name >> group; m->gobble(in2);
+ newCount.setAbund(name, group, 0);
+ }
+ in2.close();
+ }
+ m->mothurRemove(accnos + ".byCount." + toString(processIDS[i]) + ".temp");
+ }
+
}
-
+
+ //print new *.pick.count_table
+ if (hasCount && dups) { newCount.printTable(newCountFile); }
+
return num;
}
projects / mothur.git / blobdiff