}
}
//**********************************************************************************************************************
+string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //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 == "fasta") { outputFileName = "fasta"; }
+ 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, "BinSeqCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(){
try {
abort = true; calledHelp = true;
}
namesfile = validParameter.validFile(parameters, "name", true);
- if (namesfile == "not open") { abort = true; }
+ if (namesfile == "not open") { namesfile = ""; abort = true; }
else if (namesfile == "not found") { namesfile = ""; }
else { m->setNameFile(namesfile); }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
+ if (namesfile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+
}
}
catch(exception& e) {
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector();
}
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
delete list;
}
delete fasta;
if (groupfile != "") { delete groupMap; }
- 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++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
//return 1 if error, 0 otherwise
int BinSeqCommand::process(ListVector* list) {
try {
- string binnames, name, sequence;
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
- m->openOutputFile(outputFileName, out);
-
- //save to output list of output file names
- outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
-
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- //for each bin in the list vector
- for (int i = 0; i < list->size(); i++) {
-
- if (m->control_pressed) { return 1; }
-
- binnames = list->get(i);
- while (binnames.find_first_of(',') != -1) {
- name = binnames.substr(0,binnames.find_first_of(','));
- binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-
- //do work for that name
- sequence = fasta->getSequence(name);
- if (sequence != "not found") {
- //if you don't have groups
- if (groupfile == "") {
- name = name + "\t" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }else {//if you do have groups
- string group = groupMap->getGroup(name);
- if (group == "not found") {
- m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }else{
- name = name + "\t" + group + "\t" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }
- }
- }else {
- m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }
-
- }
-
- //get last name
- sequence = fasta->getSequence(binnames);
- if (sequence != "not found") {
- //if you don't have groups
- if (groupfile == "") {
- binnames = binnames + "\t" + toString(i+1);
- out << ">" << binnames << endl;
- out << sequence << endl;
- }else {//if you do have groups
- string group = groupMap->getGroup(binnames);
- if (group == "not found") {
- m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }else{
- binnames = binnames + "\t" + group + "\t" + toString(i+1);
- out << ">" << binnames << endl;
- out << sequence << endl;
- }
- }
- }else {
- m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }
- }
-
- out.close();
- return 0;
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta");
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->size(); i++) {
+
+ if (m->control_pressed) { return 1; }
+
+ string binnames = list->get(i);
+ vector<string> names;
+ m->splitAtComma(binnames, names);
+ for (int j = 0; j < names.size(); j++) {
+ string name = names[j];
+
+ //do work for that name
+ string sequence = fasta->getSequence(name);
+ if (sequence != "not found") {
+ //if you don't have groups
+ if (groupfile == "") {
+ name = name + "\t" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(name);
+ if (group == "not found") {
+ m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }else{
+ name = name + "\t" + group + "\t" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }
+ }
+ }else { m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine(); return 1; }
+ }
+ }
+
+ out.close();
+ return 0;
}
catch(exception& e) {
projects / mothur.git / blobdiff