#include "deconvolutecommand.h"
#include "uc.h"
#include "sequence.hpp"
+#include "referencedb.h"
//**********************************************************************************************************************
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); }
return myArray;
//***************************************************************************************************************
ChimeraUchimeCommand::ChimeraUchimeCommand(string option) {
try {
- abort = false; calledHelp = false;
+ abort = false; calledHelp = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
//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"){ outputDir = ""; }
-
string path;
it = parameters.find("reference");
//user has given a template file
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.uchime command."); m->mothurOutEndLine(); abort = true; }
+ else if (templatefile == "not found") { //check for saved reference sequences
+ if (rdb->getSavedReference() != "") {
+ templatefile = rdb->getSavedReference();
+ m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + "."); m->mothurOutEndLine();
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ 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; }
-
-
+ else {
+ if (rdb->getSavedReference() != "") {
+ templatefile = rdb->getSavedReference();
+ m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + "."); m->mothurOutEndLine();
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ m->mothurOutEndLine();
+ templatefile = ""; abort = true;
+ }
+ }
+
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
convert(temp, processors);
temp = validParameter.validFile(parameters, "skipgaps2", false); if (temp == "not found") { temp = "t"; }
skipgaps2 = 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; }
}
}
catch(exception& e) {
while (!in.eof()) {
- if (m->control_pressed) { in.close(); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { in.close(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
Sequence seq(in); m->gobble(in);
seqs[seq.getName()] = seq.getAligned();
vector<seqPriorityNode> nameMapCount;
int error = m->readNames(nameFile, nameMapCount, seqs);
- if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
- if (error == 1) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
- if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (error == 1) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+ if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
#ifdef USE_MPI
}
#endif
- if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
}
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.accnos";
string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.alns";
- if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
int numSeqs = 0;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#else
numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName);
#endif
- if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
//remove file made for uchime
- if (templatefile == "self") { remove(fastaFileNames[s].c_str()); }
+ if (templatefile == "self") { m->mothurRemove(fastaFileNames[s]); }
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
num += temp;
m->appendFiles((outputFileName + toString(j) + ".temp"), outputFileName);
- remove((outputFileName + toString(j) + ".temp").c_str());
+ m->mothurRemove((outputFileName + toString(j) + ".temp"));
m->appendFiles((accnos + toString(j) + ".temp"), accnos);
- remove((accnos + toString(j) + ".temp").c_str());
+ m->mothurRemove((accnos + toString(j) + ".temp"));
if (chimealns) {
m->appendFiles((alns + toString(j) + ".temp"), alns);
- remove((alns + toString(j) + ".temp").c_str());
+ m->mothurRemove((alns + toString(j) + ".temp"));
}
}
}
string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
- in.close(); remove(tempFile.c_str());
+ in.close(); m->mothurRemove(tempFile);
}
//append output files
for(int i=0;i<processIDS[i];i++){
m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
- remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
- remove((accnos + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
if (chimealns) {
m->appendFiles((alns + toString(processIDS[i]) + ".temp"), alns);
- remove((alns + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((alns + toString(processIDS[i]) + ".temp"));
}
}
#endif
//get rid of the file pieces.
- for (int i = 0; i < files.size(); i++) { remove(files[i].c_str()); }
+ for (int i = 0; i < files.size(); i++) { m->mothurRemove(files[i]); }
#endif
return num;
}
projects / mothur.git / blobdiff