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 pminsmoothid("minsmoothid", "Number", "", "0.95", "", "", "",false,false); parameters.push_back(pminsmoothid);
+ //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);
helpString += "The abskew parameter can only be used with template=self. Minimum abundance skew. Default 1.9. Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query).\n";
helpString += "The chimealns parameter allows you to indicate you would like a file containing multiple alignments of query sequences to parents in human readable format. Alignments show columns with differences that support or contradict a chimeric model.\n";
helpString += "The minh parameter - mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n";
- helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease --min h, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n";
+ helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease minh, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n";
helpString += "The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.\n";
helpString += "The dn parameter - pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.\n";
helpString += "The xa parameter - weight of an abstain vote. Default 1. So far, results do not seem to be very sensitive to this parameter, but if you have a good training set might be worth trying. Reasonable values might range from 0.1 to 2.\n";
helpString += "The chunks parameter is the number of chunks to extract from the query sequence when searching for parents. Default 4.\n";
helpString += "The minchunk parameter is the minimum length of a chunk. Default 64.\n";
helpString += "The idsmoothwindow parameter is the length of id smoothing window. Default 32.\n";
- helpString += "The minsmoothid parameter - minimum factional identity over smoothed window of candidate parent. Default 0.95.\n";
+ //helpString += "The minsmoothid parameter - minimum factional identity over smoothed window of candidate parent. Default 0.95.\n";
helpString += "The maxp parameter - maximum number of candidate parents to consider. Default 2. In tests so far, increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit.\n";
helpString += "The skipgaps parameter controls how gapped columns affect counting of diffs. If skipgaps is set to T, columns containing gaps do not found as diffs. Default = T.\n";
helpString += "The skipgaps2 parameter controls how gapped columns affect counting of diffs. If skipgaps2 is set to T, if column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default = T.\n";
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
}
}
}
//erase from file list
nameFileNames.erase(nameFileNames.begin()+i);
i--;
+ }else {
+ m->setNameFile(nameFileNames[i]);
}
}
}
templatefile = validParameter.validFile(parameters, "reference", true);
if (templatefile == "not open") { abort = true; }
- else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
+ else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.uchime command."); m->mothurOutEndLine(); abort = true; }
}
- }
+ }else if (hasName) { templatefile = "self"; }
+ else { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.uchime command, unless you have a namefile."); m->mothurOutEndLine(); abort = true; }
+
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
chunks = validParameter.validFile(parameters, "chunks", false); if (chunks == "not found") { useChunks = false; chunks = "4"; } else{ useChunks = true; }
minchunk = validParameter.validFile(parameters, "minchunk", false); if (minchunk == "not found") { useMinchunk = false; minchunk = "64"; } else{ useMinchunk = true; }
idsmoothwindow = validParameter.validFile(parameters, "idsmoothwindow", false); if (idsmoothwindow == "not found") { useIdsmoothwindow = false; idsmoothwindow = "32"; } else{ useIdsmoothwindow = true; }
- minsmoothid = validParameter.validFile(parameters, "minsmoothid", false); if (minsmoothid == "not found") { useMinsmoothid = false; minsmoothid = "0.95"; } else{ useMinsmoothid = true; }
+ //minsmoothid = validParameter.validFile(parameters, "minsmoothid", false); if (minsmoothid == "not found") { useMinsmoothid = false; minsmoothid = "0.95"; } else{ useMinsmoothid = true; }
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; }
int start = time(NULL);
string nameFile = "";
- if (templatefile == "self") { //you want to run slayer with a refernce template
+ if (templatefile == "self") { //you want to run uchime with a reference template
#ifdef USE_MPI
int pid;
sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
- string newFasta = fastaFileNames[s] + ".temp";
+ string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
ofstream out;
m->openOutputFile(newFasta, out);
strcpy(tempUchime, "./uchime ");
cPara.push_back(tempUchime);
- char* tempIn = new char[7];
- strcpy(tempIn, "--input");
+ char* tempIn = new char[8];
+ *tempIn = '\0'; strncat(tempIn, "--input", 7);
+ //strcpy(tempIn, "--input");
cPara.push_back(tempIn);
- char* temp = new char[filename.length()];
- strcpy(temp, filename.c_str());
+ char* temp = new char[filename.length()+1];
+ *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
+ //strcpy(temp, filename.c_str());
cPara.push_back(temp);
//are you using a reference file
if (templatefile != "self") {
-
//add reference file
- char* tempRef = new char[4];
- strcpy(tempRef, "--db");
+ char* tempRef = new char[5];
+ //strcpy(tempRef, "--db");
+ *tempRef = '\0'; strncat(tempRef, "--db", 4);
cPara.push_back(tempRef);
- char* tempR = new char[templatefile.length()];
- strcpy(tempR, templatefile.c_str());
+ char* tempR = new char[templatefile.length()+1];
+ //strcpy(tempR, templatefile.c_str());
+ *tempR = '\0'; strncat(tempR, templatefile.c_str(), templatefile.length());
cPara.push_back(tempR);
}
- char* tempO = new char[11];
- strcpy(tempO, "--uchimeout");
+ char* tempO = new char[12];
+ *tempO = '\0'; strncat(tempO, "--uchimeout", 11);
+ //strcpy(tempO, "--uchimeout");
cPara.push_back(tempO);
- char* tempout = new char[outputFName.length()];
- strcpy(tempout, outputFName.c_str());
+ char* tempout = new char[outputFName.length()+1];
+ //strcpy(tempout, outputFName.c_str());
+ *tempout = '\0'; strncat(tempout, outputFName.c_str(), outputFName.length());
cPara.push_back(tempout);
if (chimealns) {
- char* tempA = new char[12];
- strcpy(tempA, "--uchimealns");
+ char* tempA = new char[13];
+ *tempA = '\0'; strncat(tempA, "--uchimealns", 12);
+ //strcpy(tempA, "--uchimealns");
cPara.push_back(tempA);
- char* tempa = new char[alns.length()];
- strcpy(tempa, alns.c_str());
+ char* tempa = new char[alns.length()+1];
+ //strcpy(tempa, alns.c_str());
+ *tempa = '\0'; strncat(tempa, alns.c_str(), alns.length());
cPara.push_back(tempa);
}
if (useAbskew) {
- char* tempskew = new char[8];
- strcpy(tempskew, "--abskew");
+ char* tempskew = new char[9];
+ *tempskew = '\0'; strncat(tempskew, "--abskew", 8);
+ //strcpy(tempskew, "--abskew");
cPara.push_back(tempskew);
- char* tempSkew = new char[abskew.length()];
- strcpy(tempSkew, abskew.c_str());
+ char* tempSkew = new char[abskew.length()+1];
+ //strcpy(tempSkew, abskew.c_str());
+ *tempSkew = '\0'; strncat(tempSkew, abskew.c_str(), abskew.length());
cPara.push_back(tempSkew);
}
if (useMinH) {
- char* tempminh = new char[6];
- strcpy(tempminh, "--minh");
+ char* tempminh = new char[7];
+ *tempminh = '\0'; strncat(tempminh, "--minh", 6);
+ //strcpy(tempminh, "--minh");
cPara.push_back(tempminh);
- char* tempMinH = new char[minh.length()];
- strcpy(tempMinH, minh.c_str());
+ char* tempMinH = new char[minh.length()+1];
+ *tempMinH = '\0'; strncat(tempMinH, minh.c_str(), minh.length());
+ //strcpy(tempMinH, minh.c_str());
cPara.push_back(tempMinH);
}
if (useMindiv) {
- char* tempmindiv = new char[8];
- strcpy(tempmindiv, "--mindiv");
+ char* tempmindiv = new char[9];
+ *tempmindiv = '\0'; strncat(tempmindiv, "--mindiv", 8);
+ //strcpy(tempmindiv, "--mindiv");
cPara.push_back(tempmindiv);
- char* tempMindiv = new char[mindiv.length()];
- strcpy(tempMindiv, mindiv.c_str());
+ char* tempMindiv = new char[mindiv.length()+1];
+ *tempMindiv = '\0'; strncat(tempMindiv, mindiv.c_str(), mindiv.length());
+ //strcpy(tempMindiv, mindiv.c_str());
cPara.push_back(tempMindiv);
}
if (useXn) {
- char* tempxn = new char[4];
- strcpy(tempxn, "--xn");
+ char* tempxn = new char[5];
+ //strcpy(tempxn, "--xn");
+ *tempxn = '\0'; strncat(tempxn, "--xn", 4);
cPara.push_back(tempxn);
- char* tempXn = new char[xn.length()];
- strcpy(tempXn, xn.c_str());
+ char* tempXn = new char[xn.length()+1];
+ //strcpy(tempXn, xn.c_str());
+ *tempXn = '\0'; strncat(tempXn, xn.c_str(), xn.length());
cPara.push_back(tempXn);
}
if (useDn) {
- char* tempdn = new char[4];
- strcpy(tempdn, "--dn");
+ char* tempdn = new char[5];
+ //strcpy(tempdn, "--dn");
+ *tempdn = '\0'; strncat(tempdn, "--dn", 4);
cPara.push_back(tempdn);
- char* tempDn = new char[dn.length()];
- strcpy(tempDn, dn.c_str());
+ char* tempDn = new char[dn.length()+1];
+ *tempDn = '\0'; strncat(tempDn, dn.c_str(), dn.length());
+ //strcpy(tempDn, dn.c_str());
cPara.push_back(tempDn);
}
if (useXa) {
- char* tempxa = new char[4];
- strcpy(tempxa, "--xa");
+ char* tempxa = new char[5];
+ //strcpy(tempxa, "--xa");
+ *tempxa = '\0'; strncat(tempxa, "--xa", 4);
cPara.push_back(tempxa);
- char* tempXa = new char[xa.length()];
- strcpy(tempXa, xa.c_str());
+ char* tempXa = new char[xa.length()+1];
+ *tempXa = '\0'; strncat(tempXa, xa.c_str(), xa.length());
+ //strcpy(tempXa, xa.c_str());
cPara.push_back(tempXa);
}
if (useChunks) {
- char* tempchunks = new char[8];
- strcpy(tempchunks, "--chunks");
+ char* tempchunks = new char[9];
+ //strcpy(tempchunks, "--chunks");
+ *tempchunks = '\0'; strncat(tempchunks, "--chunks", 8);
cPara.push_back(tempchunks);
- char* tempChunks = new char[chunks.length()];
- strcpy(tempChunks, chunks.c_str());
+ char* tempChunks = new char[chunks.length()+1];
+ *tempChunks = '\0'; strncat(tempChunks, chunks.c_str(), chunks.length());
+ //strcpy(tempChunks, chunks.c_str());
cPara.push_back(tempChunks);
}
if (useMinchunk) {
- char* tempminchunk = new char[10];
- strcpy(tempminchunk, "--minchunk");
+ char* tempminchunk = new char[11];
+ //strcpy(tempminchunk, "--minchunk");
+ *tempminchunk = '\0'; strncat(tempminchunk, "--minchunk", 10);
cPara.push_back(tempminchunk);
- char* tempMinchunk = new char[minchunk.length()];
- strcpy(tempMinchunk, minchunk.c_str());
+ char* tempMinchunk = new char[minchunk.length()+1];
+ *tempMinchunk = '\0'; strncat(tempMinchunk, minchunk.c_str(), minchunk.length());
+ //strcpy(tempMinchunk, minchunk.c_str());
cPara.push_back(tempMinchunk);
}
if (useIdsmoothwindow) {
- char* tempidsmoothwindow = new char[16];
- strcpy(tempidsmoothwindow, "--idsmoothwindow");
+ char* tempidsmoothwindow = new char[17];
+ *tempidsmoothwindow = '\0'; strncat(tempidsmoothwindow, "--idsmoothwindow", 16);
+ //strcpy(tempidsmoothwindow, "--idsmoothwindow");
cPara.push_back(tempidsmoothwindow);
- char* tempIdsmoothwindow = new char[idsmoothwindow.length()];
- strcpy(tempIdsmoothwindow, idsmoothwindow.c_str());
+ char* tempIdsmoothwindow = new char[idsmoothwindow.length()+1];
+ *tempIdsmoothwindow = '\0'; strncat(tempIdsmoothwindow, idsmoothwindow.c_str(), idsmoothwindow.length());
+ //strcpy(tempIdsmoothwindow, idsmoothwindow.c_str());
cPara.push_back(tempIdsmoothwindow);
}
- if (useMinsmoothid) {
- char* tempminsmoothid = new char[13];
- strcpy(tempminsmoothid, "--minsmoothid");
+ /*if (useMinsmoothid) {
+ char* tempminsmoothid = new char[14];
+ //strcpy(tempminsmoothid, "--minsmoothid");
+ *tempminsmoothid = '\0'; strncat(tempminsmoothid, "--minsmoothid", 13);
cPara.push_back(tempminsmoothid);
- char* tempMinsmoothid = new char[minsmoothid.length()];
- strcpy(tempMinsmoothid, minsmoothid.c_str());
+ char* tempMinsmoothid = new char[minsmoothid.length()+1];
+ *tempMinsmoothid = '\0'; strncat(tempMinsmoothid, minsmoothid.c_str(), minsmoothid.length());
+ //strcpy(tempMinsmoothid, minsmoothid.c_str());
cPara.push_back(tempMinsmoothid);
- }
+ }*/
if (useMaxp) {
- char* tempmaxp = new char[6];
- strcpy(tempmaxp, "--maxp");
+ char* tempmaxp = new char[7];
+ //strcpy(tempmaxp, "--maxp");
+ *tempmaxp = '\0'; strncat(tempmaxp, "--maxp", 6);
cPara.push_back(tempmaxp);
- char* tempMaxp = new char[maxp.length()];
- strcpy(tempMaxp, maxp.c_str());
+ char* tempMaxp = new char[maxp.length()+1];
+ *tempMaxp = '\0'; strncat(tempMaxp, maxp.c_str(), maxp.length());
+ //strcpy(tempMaxp, maxp.c_str());
cPara.push_back(tempMaxp);
}
if (!skipgaps) {
- char* tempskipgaps = new char[14];
- strcpy(tempskipgaps, "--[no]skipgaps");
+ char* tempskipgaps = new char[13];
+ //strcpy(tempskipgaps, "--[no]skipgaps");
+ *tempskipgaps = '\0'; strncat(tempskipgaps, "--noskipgaps", 12);
cPara.push_back(tempskipgaps);
}
if (!skipgaps2) {
- char* tempskipgaps2 = new char[15];
- strcpy(tempskipgaps2, "--[no]skipgaps2");
+ char* tempskipgaps2 = new char[14];
+ //strcpy(tempskipgaps2, "--[no]skipgaps2");
+ *tempskipgaps2 = '\0'; strncat(tempskipgaps2, "--noskipgaps2", 13);
cPara.push_back(tempskipgaps2);
}
if (useMinlen) {
- char* tempminlen = new char[8];
- strcpy(tempminlen, "--minlen");
+ char* tempminlen = new char[9];
+ *tempminlen = '\0'; strncat(tempminlen, "--minlen", 8);
+ //strcpy(tempminlen, "--minlen");
cPara.push_back(tempminlen);
- char* tempMinlen = new char[minlen.length()];
- strcpy(tempMinlen, minlen.c_str());
+ char* tempMinlen = new char[minlen.length()+1];
+ //strcpy(tempMinlen, minlen.c_str());
+ *tempMinlen = '\0'; strncat(tempMinlen, minlen.c_str(), minlen.length());
cPara.push_back(tempMinlen);
}
if (useMaxlen) {
- char* tempmaxlen = new char[8];
- strcpy(tempmaxlen, "--maxlen");
+ char* tempmaxlen = new char[9];
+ //strcpy(tempmaxlen, "--maxlen");
+ *tempmaxlen = '\0'; strncat(tempmaxlen, "--maxlen", 8);
cPara.push_back(tempmaxlen);
- char* tempMaxlen = new char[maxlen.length()];
- strcpy(tempMaxlen, maxlen.c_str());
+ char* tempMaxlen = new char[maxlen.length()+1];
+ *tempMaxlen = '\0'; strncat(tempMaxlen, maxlen.c_str(), maxlen.length());
+ //strcpy(tempMaxlen, maxlen.c_str());
cPara.push_back(tempMaxlen);
}
}
if (useQueryfract) {
- char* tempqueryfract = new char[12];
- strcpy(tempqueryfract, "--queryfract");
+ char* tempqueryfract = new char[13];
+ *tempqueryfract = '\0'; strncat(tempqueryfract, "--queryfract", 12);
+ //strcpy(tempqueryfract, "--queryfract");
cPara.push_back(tempqueryfract);
- char* tempQueryfract = new char[queryfract.length()];
- strcpy(tempQueryfract, queryfract.c_str());
+ char* tempQueryfract = new char[queryfract.length()+1];
+ *tempQueryfract = '\0'; strncat(tempQueryfract, queryfract.c_str(), queryfract.length());
+ //strcpy(tempQueryfract, queryfract.c_str());
cPara.push_back(tempQueryfract);
}
for(int i = 0; i < cPara.size(); i++) { delete[] cPara[i]; }
delete[] uchimeParameters;
+ if (m->control_pressed) { return 0; }
+
//create accnos file from uchime results
ifstream in;
m->openInputFile(outputFName, in);
in >> chimeraFlag >> name;
//fix name if needed
- if (templatefile != "self") {
+ if (templatefile == "self") {
name = name.substr(0, name.length()-1); //rip off last /
name = name.substr(0, name.find_last_of('/'));
}
processIDS.clear();
int process = 1;
int num = 0;
-
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//break up file into multiple files
vector<string> files;
m->divideFile(filename, processors, files);
#endif
//get rid of the file pieces.
for (int i = 0; i < files.size(); i++) { remove(files[i].c_str()); }
-
+#endif
return num;
}
catch(exception& e) {
projects / mothur.git / blobdiff