#include "readotucommand.h"
//**********************************************************************************************************************
-ReadOtuCommand::ReadOtuCommand(string option){
+ReadOtuCommand::ReadOtuCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
else {
//valid paramters for this command
- string Array[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
+ 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;
}
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ 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 == "")) {
- mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true;
+ m->mothurOut("You must enter either a listfile, rabundfile, sabundfile 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 {
}
globaldata->allLines = allLines;
-
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); 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;
}
-
}
}
catch(exception& e) {
- errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+ m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
exit(1);
}
}
void ReadOtuCommand::help(){
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, line and label.\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("The line and label parameters are optional but you may not use both the line and label parameters at the same time.\n");
- mothurOut("The label and line parameters are used to read specific lines in your input.\n");
- mothurOut("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");
- mothurOut("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");
- 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 .list file for each group. \n");
- mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
+ m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
+ m->mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
+ m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, label and groups.\n");
+ m->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");
+ m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
+ m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
+ m->mothurOut("The label parameter is used to read specific labels in your input.\n");
+ m->mothurOut("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");
+ m->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");
+ m->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");
+ m->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");
+ m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
}
catch(exception& e) {
- errorOut(e, "ReadOtuCommand", "help");
+ m->errorOut(e, "ReadOtuCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
-
-ReadOtuCommand::~ReadOtuCommand(){
- }
-
+ReadOtuCommand::~ReadOtuCommand(){}
//**********************************************************************************************************************
int ReadOtuCommand::execute(){
try {
if (abort == true) { return 0; }
-
+
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");
+ }else { //shared command outputs the filenames
+ //m->mothurOutEndLine();
+ //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
+ //m->mothurOutEndLine();
}
+
+ delete shared;
}
return 0;
}
catch(exception& e) {
- errorOut(e, "ReadOtuCommand", "execute");
+ m->errorOut(e, "ReadOtuCommand", "execute");
exit(1);
}
}
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