vector<string> ParseListCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+ CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "CountGroup", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "CountGroup", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
string ParseListCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n";
- helpString += "The parse.list command parameters are list, group and label.\n";
- helpString += "The list and group parameters are required.\n";
+ helpString += "The parse.list command reads a list and group or count file and generates a list file for each group in the group or count file. \n";
+ helpString += "The parse.list command parameters are list, group, count and label.\n";
+ helpString += "The list and group or count parameters are required.\n";
+ helpString += "If a count file is provided, mothur assumes the list file contains only unique names.\n";
+ helpString += "If a group file is provided, mothur assumes the list file contains all names.\n";
helpString += "The label parameter is used to read specific labels in your input you want to use.\n";
helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n";
helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n";
//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("count");
+ //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["count"] = 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);
}
}else { m->setListFile(listfile); }
+
+ //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 = m->hasPath(listfile); }
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") {
- groupfile = m->getListFile();
- if (groupfile != "") {
- m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine();
- groupMap = new GroupMap(groupfile);
-
- int error = groupMap->readMap();
- if (error == 1) { abort = true; }
- }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); abort = true; }
- }else {
- m->setGroupFile(groupfile);
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not found") { groupfile = ""; groupMap = NULL; }
+ else if (groupfile == "not open") { abort = true; groupfile = ""; groupMap = NULL; }
+ else {
+ m->setGroupFile(groupfile);
groupMap = new GroupMap(groupfile);
int error = groupMap->readMap();
if (error == 1) { abort = true; }
- }
-
- //do you have all files needed
- if ((listfile == "") || (groupfile == "")) { m->mothurOut("You must enter both a listfile and groupfile for the parse.list command. "); m->mothurOutEndLine(); abort = true; }
+ }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not found") { countfile = ""; }
+ else if (countfile == "not open") { abort = true; countfile = ""; }
+ else {
+ m->setCountTableFile(countfile);
+ ct.readTable(countfile);
+ if (!ct.hasGroupInfo()) {
+ abort = true;
+ m->mothurOut("[ERROR]: The parse.list command requires group info to be present in your countfile, quitting."); m->mothurOutEndLine();
+ }
+
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }else if ((groupfile == "") && (countfile == "")) {
+ m->mothurOut("[ERROR]: you must provide one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
//fill filehandles with neccessary ofstreams
int i;
ofstream* temp;
- vector<string> gGroups = groupMap->getNamesOfGroups();
+ vector<string> gGroups;
+ if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); }
+ else { gGroups = ct.getNamesOfGroups(); }
+
for (i=0; i<gGroups.size(); i++) {
temp = new ofstream;
filehandles[gGroups[i]] = temp;
set<string> processedLabels;
set<string> userLabels = labels;
- input = new InputData(listfile, "list");
- list = input->getListVector();
+ InputData input(listfile, "list");
+ list = input.getListVector();
string lastLabel = list->getLabel();
if (m->control_pressed) {
- delete input; delete list; delete groupMap;
- vector<string> gGroups = groupMap->getNamesOfGroups();
+ delete list; if (groupfile != "") { delete groupMap; }
for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
- delete input; delete list; delete groupMap;
+ delete list; if (groupfile != "") { delete groupMap; }
for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
- delete list;
- list = input->getListVector(lastLabel); //get new list vector to process
+ list = input.getListVector(lastLabel); //get new list vector to process
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
parse(list);
lastLabel = list->getLabel();
delete list;
- list = input->getListVector(); //get new list vector to process
+ list = input.getListVector(); //get new list vector to process
}
if (m->control_pressed) {
- delete input; delete groupMap;
+ if (groupfile != "") { delete groupMap; }
for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
if (m->control_pressed) {
- delete input; delete groupMap;
+ if (groupfile != "") { delete groupMap; }
for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
- list = input->getListVector(lastLabel); //get new list vector to process
+ list = input.getListVector(lastLabel); //get new list vector to process
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
parse(list);
delete it3->second;
}
-
- delete groupMap;
- delete input;
+ if (groupfile != "") { delete groupMap; }
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
//parse bin into list of sequences in each group
for (int j = 0; j < names.size(); j++) {
- string group = groupMap->getGroup(names[j]);
+ if (groupfile != "") {
+ string group = groupMap->getGroup(names[j]);
- if (group == "not found") { m->mothurOut(names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); exit(1); }
+ if (group == "not found") { m->mothurOut(names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); exit(1); }
- itGroup = groupBins.find(group);
- if(itGroup == groupBins.end()) {
- groupBins[group] = names[j]; //add first name
- groupNumBins[group]++;
- }else{ //add another name
- groupBins[group] = groupBins[group] + "," + names[j];
- }
+ itGroup = groupBins.find(group);
+ if(itGroup == groupBins.end()) {
+ groupBins[group] = names[j]; //add first name
+ groupNumBins[group]++;
+ }else{ //add another name
+ groupBins[group] = groupBins[group] + "," + names[j];
+ }
+ }else{
+ vector<string> thisSeqsGroups = ct.getGroups(names[j]);
+
+ for (int k = 0; k < thisSeqsGroups.size(); k++) {
+ string group = thisSeqsGroups[k];
+ itGroup = groupBins.find(group);
+ if(itGroup == groupBins.end()) {
+ groupBins[group] = names[j]; //add first name
+ groupNumBins[group]++;
+ }else{ //add another name
+ groupBins[group] = groupBins[group] + "," + names[j];
+ }
+
+ }
+ }
}
//print parsed bin info to files
projects / mothur.git / blobdiff