#include "readotucommand.h"
+
+//**********************************************************************************************************************
+ReadOtuCommand::ReadOtuCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-ReadOtuCommand::ReadOtuCommand(string option){
+ReadOtuCommand::ReadOtuCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
+ /*
//valid paramters for this command
- string Array[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
+ string Array[] = {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/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; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+
globaldata->newRead();
+ //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; }
+ }
+
+ it = parameters.find("order");
+ //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["order"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("shared");
+ //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["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //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["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //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["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("ordergroup");
+ //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["ordergroup"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("relabund");
+ //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["relabund"] = 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 open") { abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");}
+ ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
+ if (ordergroupfile == "not open") { abort = true; }
+ else if (ordergroupfile == "not found") { ordergroupfile = ""; }
+ else { globaldata->setOrderGroupFile(ordergroupfile); }
+
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile"); }
+ relAbundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relAbundfile == "not open") { abort = true; }
+ else if (relAbundfile == "not found") { relAbundfile = ""; }
+ else { globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund"); }
+
+
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else {
globaldata->setGroupFile(groupfile);
groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+
+ globaldata->gGroupmap = groupMap;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
}
//you are doing a list and group shared
if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
//you have not given a file
- if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
- cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; abort = true;
+ if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) {
+ m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- globaldata->lines = lines;
- }
-
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; }
globaldata->labels = labels;
}
globaldata->allLines = allLines;
-
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
-
+
orderfile = validParameter.validFile(parameters, "order", true);
if (orderfile == "not open") { abort = true; }
else if (orderfile == "not found") { orderfile = ""; }
else { globaldata->setOrderFile(orderfile); }
-
+
if (abort == false) {
//gets whichever one of the above is set
filename = globaldata->inputFileName;
- //read = new ReadOTUFile(filename);
}
-
+ */
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void ReadOtuCommand::help(){
- try {
- cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
- cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
- cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n";
- cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
- cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n";
- cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
- cout << "The line and label parameters are optional but you may not use both the line and label parameters at the same time." << "\n";
- cout << "The label and line parameters are used to read specific lines in your input." << "\n";
- cout << "The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n";
- cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). " << "\n";
- cout << "The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file" << "\n";
- cout << "and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n";
- cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
-
-
-//**********************************************************************************************************************
-
-ReadOtuCommand::~ReadOtuCommand(){
- if (abort == false) { //delete read;
- }
-}
-
-//**********************************************************************************************************************
+///**********************************************************************************************************************
int ReadOtuCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- //read->read(&*globaldata);
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->mothurOut(getHelpString()); m->mothurOutEndLine();
+
+ /*
if (globaldata->getFormat() == "shared") {
- groupMap->readMap();
- //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
- globaldata->gGroupmap = groupMap;
+ shared = new SharedCommand(outputDir);
+ int okay = shared->execute();
+
+ //problem with shared
+ if (okay == 1) {
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
+ globaldata->setSharedFile("");
+ }else { //shared command outputs the filenames
+ //m->mothurOutEndLine();
+ //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
+ //m->mothurOutEndLine();
+ }
- parselist = new ParseListCommand();
- parselist->execute();
- delete parselist;
+ outputTypes = shared->getOutputFiles();
- shared = new SharedCommand();
- shared->execute();
- delete shared;
+ //set rabund file as new current rabundfile
+ string current = "";
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ itTypes = outputTypes.find("shared");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+ }
- //change format to shared to speed up commands
- globaldata->setFormat("sharedfile");
- globaldata->setListFile("");
- globaldata->setGroupFile("");
- globaldata->setSharedFile(getRootName(filename) + "shared");
+ delete shared;
}
+ */
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReadOtuCommand", "execute");
exit(1);
}
}
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