else {
//valid paramters for this command
- string Array[] = {"list","order","shared", "label","group","sabund", "rabund","groups"};
+ string Array[] = {"list","order","shared", "label","group","sabund", "rabund","groups","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; }
}
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 = 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 = 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 = 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 = 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 = 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 = 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; }
+ }
+
+ }
+
+
+ //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 {
globaldata->setGroupFile(groupfile);
groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+
globaldata->gGroupmap = groupMap;
}
try {
mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
- mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order and label.\n");
+ mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, label and groups.\n");
mothurOut("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");
mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile) or read.otu(shared=yourSharedFile). \n");
mothurOut("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");
mothurOut("and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .rabund file for each group. \n");
+ mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
}
if (globaldata->getFormat() == "shared") {
- shared = new SharedCommand();
+ shared = new SharedCommand(outputDir);
int okay = shared->execute();
- delete shared;
//problem with shared
if (okay == 1) {
globaldata->setListFile("");
globaldata->setGroupFile("");
globaldata->setSharedFile("");
- }else{
-
- //change format to shared to speed up commands
- globaldata->setFormat("sharedfile");
- globaldata->setListFile("");
- globaldata->setGroupFile("");
- globaldata->setSharedFile(getRootName(filename) + "shared");
}
+
+ delete shared;
}
return 0;
}
projects / mothur.git / blobdiff