globaldata = GlobalData::getInstance();
fastafile = globaldata->getFastaFile();
namesfile = globaldata->getNameFile();
+ groupfile = globaldata->getGroupFile();
openInputFile(fastafile, in);
+ if (groupfile != "") {
+ //read in group map info.
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+ }
+
fasta = new FastaMap();
}
catch(exception& e) {
delete read;
delete fasta;
delete list;
+ if (groupfile != "") {
+ delete groupMap;
+ }
}
//**********************************************************************************************************************
int BinSeqCommand::execute(){
try {
int count = 1;
- string binnames, name, sequence;
+ int error = 0;
//read fastafile
fasta->readFastaFile(in);
}
//read list file
- read = new ReadPhilFile(globaldata->getListFile());
+ read = new ReadOTUFile(globaldata->getListFile());
read->read(&*globaldata);
input = globaldata->ginput;
list = globaldata->gListVector;
+ ListVector* lastList = list;
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+ set<int> userLines = globaldata->lines;
+
- while(list != NULL){
+ while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
- //create output file
- string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
- openOutputFile(outputFileName, out);
-
- cout << list->getLabel() << '\t' << count << endl;
+ error = process(list, count);
+ if (error == 1) { return 0; }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+
+ error = process(lastList, count);
+ if (error == 1) { return 0; }
+
+ processedLabels.insert(lastList->getLabel());
+ userLabels.erase(lastList->getLabel());
- //for each bin in the list vector
- for (int i = 0; i < list->size(); i++) {
- 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") {
- name = name + "bin" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }else {
- cout << name << " is missing from your fasta or name file. Please correct. " << endl;
- remove(outputFileName.c_str());
- return 0;
- }
-
- }
-
- //get last name
- sequence = fasta->getSequence(binnames);
- if (sequence != "not found") {
- name = binnames + "bin" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }else {
- cout << binnames << " is missing from your fasta or name file. Please correct. " << endl;
- remove(outputFileName.c_str());
- return 0;
- }
- }
}
+ if (count != 1) { delete lastList; }
+ lastList = list;
+
list = input->getListVector();
count++;
}
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastList->getLabel()) != 1) {
+ cout << ". I will use " << lastList->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ error = process(lastList, count);
+ if (error == 1) { return 0; }
+ }
+
+ delete lastList;
return 0;
}
catch(exception& e) {
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the BinSeqCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the BinSeqCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+int BinSeqCommand::process(ListVector* list, int count) {
+ try {
+ string binnames, name, sequence;
+ string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
+ openOutputFile(outputFileName, out);
+
+ cout << list->getLabel() << '\t' << count << endl;
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->size(); i++) {
+
+ 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 + "|" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(name);
+ if (group == "not found") {
+ cout << name << " is missing from your group file. Please correct. " << endl;
+ remove(outputFileName.c_str());
+ return 1;
+ }else{
+ name = name + "|" + group + "|" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }
+ }
+ }else {
+ cout << name << " is missing from your fasta or name file. Please correct. " << endl;
+ remove(outputFileName.c_str());
+ return 1;
+ }
+
+ }
+
+ //get last name
+ sequence = fasta->getSequence(binnames);
+ if (sequence != "not found") {
+ //if you don't have groups
+ if (groupfile == "") {
+ binnames = binnames + "|" + toString(i+1);
+ out << ">" << binnames << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(binnames);
+ if (group == "not found") {
+ cout << binnames << " is missing from your group file. Please correct. " << endl;
+ remove(outputFileName.c_str());
+ return 1;
+ }else{
+ binnames = binnames + "|" + group + "|" + toString(i+1);
+ out << ">" << binnames << endl;
+ out << sequence << endl;
+ }
+ }
+ }else {
+ cout << binnames << " is missing from your fasta or name file. Please correct. " << endl;
+ remove(outputFileName.c_str());
+ return 1;
+ }
+ }
+
+ out.close();
+ return 0;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BinSeqCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff