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/*
* getlistcountcommand.cpp
* Mothur
*
* Created by westcott on 10/12/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "getlistcountcommand.h"
//**********************************************************************************************************************
vector<string> GetListCountCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otu",false,true, true); parameters.push_back(plist);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "","",false,false); parameters.push_back(parasort);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false; allLines = true;
vector<string> tempOutNames;
outputTypes["otu"] = tempOutNames;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "GetListCountCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string GetListCountCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.otulist command parameters are list, sort and label. list is required, unless you have a valid current list file.\n";
helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
helpString += "The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n";
helpString += "If otu is selected the output will be otu number followed by the list of names in that otu.\n";
helpString += "If name is selected the output will be a sequence name followed by its otu number.\n";
helpString += "The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n";
helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n";
helpString += "The default value for label is all lines in your inputfile.\n";
helpString += "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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "GetListCountCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string GetListCountCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "otu") { pattern = "[filename],[tag],otu"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "GetListCountCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
GetListCountCommand::GetListCountCommand(string option) : Command() {
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
//check for required parameters
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not found") {
listfile = current->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter.\n"); }
else { m->mothurOut("You have no current list file and the list parameter is required.\n"); abort = true; }
}
else if (listfile == "not open") { abort = true; }
else { current->setListFile(listfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
sort = validParameter.valid(parameters, "sort"); 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.\n"); sort = "otu"; }
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
}
}
catch(exception& e) {
m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetListCountCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
InputData input(listfile, "list", nullVector);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
ListVector* list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
while (list != nullptr) {
if (m->getControl_pressed()) { delete list; break; }
process(list); delete list;
list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
}
if (m->getControl_pressed()) { return 0; }
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetListCountCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
//return 1 if error, 0 otherwise
void GetListCountCommand::process(ListVector* list) {
try {
string binnames;
if (outputdir == "") { outputdir += util.hasPath(listfile); }
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(listfile));
variables["[tag]"] = list->getLabel();
string outputFileName = getOutputFileName("otu", variables);
util.openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
//for each bin in the list vector
vector<string> binLabels = list->getLabels();
for (int i = 0; i < list->getNumBins(); i++) {
if (m->getControl_pressed()) { break; }
binnames = list->get(i);
if (sort == "otu") {
out << binLabels[i] << '\t' << binnames << endl;
}else{ //sort = name
vector<string> names;
util.splitAtComma(binnames, names);
for (int j = 0; j < names.size(); j++) {
out << names[j] << '\t' << binLabels[i] << endl;
}
}
}
out.close();
}
catch(exception& e) {
m->errorOut(e, "GetListCountCommand", "process");
exit(1);
}
}
//**********************************************************************************************************************
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