else {
//valid paramters for this command
- string AlignArray[] = {"list","label","outputdir","inputdir"};
+ string AlignArray[] = {"list","label","sort","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
+ sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; }
+ if ((sort != "otu") && (sort != "name")) { m->mothurOut( sort + " is not a valid sort option. Options are otu and name. I will use otu."); m->mothurOutEndLine(); sort = "otu"; }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
void GetListCountCommand::help(){
try {
- m->mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n");
- m->mothurOut("The get.listcount command parameters are list and label. No parameters are required.\n");
+ m->mothurOut("The get.otulist command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n");
+ m->mothurOut("The get.otulist command parameters are list, sort and label. No parameters are required.\n");
m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
- m->mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n");
- m->mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n");
+ m->mothurOut("The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n");
+ m->mothurOut("If otu is selected the output will be otu number followed by the list of names in that otu.\n");
+ m->mothurOut("If name is selected the output will be a sequence name followed by its otu number.\n");
+ m->mothurOut("The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n");
+ m->mothurOut("Example get.otulist(list=amazon.fn.list, label=0.10).\n");
m->mothurOut("The default value for label is all lines in your inputfile.\n");
- m->mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n");
+ m->mothurOut("The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
}
catch(exception& e) {
//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 = labels;
-
+
+ if (m->control_pressed) {
+ delete read;
+ delete input;
+ delete list;
+ globaldata->gListVector = NULL;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(list->getLabel()) == 1){
process(list);
+
+ if (m->control_pressed) {
+ delete read;
+ delete input;
+ delete list;
+ globaldata->gListVector = NULL;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input->getListVector(lastLabel);
process(list);
+
+ if (m->control_pressed) {
+ delete read;
+ delete input;
+ delete list;
+ globaldata->gListVector = NULL;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
- process(list);
+ process(list);
+
+ if (m->control_pressed) {
+ delete read;
+ delete input;
+ delete list;
+ globaldata->gListVector = NULL;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
delete list;
}
delete read;
+ delete input;
globaldata->gListVector = NULL;
m->mothurOutEndLine();
//return 1 if error, 0 otherwise
void GetListCountCommand::process(ListVector* list) {
try {
- string binnames, name, sequence;
- if (outputDir == "") { outputDir += hasPath(listfile); }
- string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + list->getLabel() + ".otu";
- openOutputFile(outputFileName, out);
+ string binnames;
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
+ m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
//for each bin in the list vector
for (int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
binnames = list->get(i);
- out << i+1 << '\t' << binnames << endl;
+
+ if (sort == "otu") {
+ out << i+1 << '\t' << binnames << endl;
+ }else{ //sort = name
+ vector<string> names;
+ m->splitAtComma(binnames, names);
+
+ for (int j = 0; j < names.size(); j++) {
+ out << names[j] << '\t' << i+1 << endl;
+ }
+ }
}
out.close();
projects / mothur.git / blobdiff