#include "readotucommand.h"
//**********************************************************************************************************************
-ReadOtuCommand::ReadOtuCommand(){
+ReadOtuCommand::ReadOtuCommand(string option){
try {
globaldata = GlobalData::getInstance();
- filename = globaldata->inputFileName;
- read = new ReadOTUFile(filename);
- if (globaldata->getFormat() == "shared") {
- //read in group map info.
- groupMap = new GroupMap(globaldata->getGroupFile());
+ abort = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ globaldata->newRead();
+
+ //check for required parameters
+ listfile = validParameter->validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { globaldata->setListFile(listfile); globaldata->setFormat("list"); }
+
+ sabundfile = validParameter->validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
+
+ rabundfile = validParameter->validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { abort = true; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+ else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");}
+
+ 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"); }
+
+ 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();
+ }
+
+ //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;
+ }
+
+ //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; }
+ 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); }
+
+ delete validParameter;
+
+ 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);
}
}
+//**********************************************************************************************************************
+
+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";
+ 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(){
- delete read;
+ if (abort == false) { delete read; }
}
//**********************************************************************************************************************
int ReadOtuCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
read->read(&*globaldata);
if (globaldata->getFormat() == "shared") {
groupMap->readMap();
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