#include "getlistcountcommand.h"
//**********************************************************************************************************************
-GetListCountCommand::GetListCountCommand(string option){
+GetListCountCommand::GetListCountCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
labels.clear();
-
+
//allow user to run help
if(option == "help") { help(); abort = true; }
else {
//valid paramters for this command
- string AlignArray[] = {"list","label"};
+ string AlignArray[] = {"list","label","sort","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
-
+ map<string, string>::iterator it;
+
//check to make sure all parameters are valid for command
- for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
string ranRead = globaldata->getListFile();
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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; }
+ }
+ }
+
+ //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 = ""; }
+
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
- if ((listfile == "not found") && (globaldata->getListFile() == "")) { mothurOut("You must read a listfile before running the get.listcount command."); mothurOutEndLine(); abort = true; }
+ if ((listfile == "not found") && (globaldata->getListFile() == "")) { m->mothurOut("You must read a listfile before running the get.listcount command."); m->mothurOutEndLine(); abort = true; }
else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); }
else if (listfile == "not open") { abort = true; }
else { globaldata->setListFile(listfile); }
//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; }
}
}
}
catch(exception& e) {
- errorOut(e, "GetListCountCommand", "GetListCountCommand");
+ m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
exit(1);
}
}
void GetListCountCommand::help(){
try {
- 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");
- mothurOut("The get.listcount command parameters are list and label. No parameters are required.\n");
- 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");
- mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n");
- mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n");
- mothurOut("The default value for label is all lines in your inputfile.\n");
- 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");
- mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\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 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.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) {
- errorOut(e, "GetListCountCommand", "help");
+ m->errorOut(e, "GetListCountCommand", "help");
exit(1);
}
}
//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());
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
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();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "GetListCountCommand", "execute");
+ m->errorOut(e, "GetListCountCommand", "execute");
exit(1);
}
}
//return 1 if error, 0 otherwise
void GetListCountCommand::process(ListVector* list) {
try {
- string binnames, name, sequence;
- string outputFileName = getRootName(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);
- mothurOut(list->getLabel()); mothurOutEndLine();
+ 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();
}
catch(exception& e) {
- errorOut(e, "GetListCountCommand", "process");
+ m->errorOut(e, "GetListCountCommand", "process");
exit(1);
}
}
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