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";
try {
string pattern = "";
- if (type == "list") { pattern = "[filename],[group],list"; }
+ if (type == "list") { pattern = "[filename],[group],[distance],list"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
//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, true, false);
+ 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...
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- //set fileroot
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
-
- //fill filehandles with neccessary ofstreams
- int i;
- ofstream* temp;
- vector<string> gGroups = groupMap->getNamesOfGroups();
- for (i=0; i<gGroups.size(); i++) {
- temp = new ofstream;
- filehandles[gGroups[i]] = temp;
-
- variables["[group]"] = gGroups[i];
- string filename = getOutputFileName("list",variables);
- outputNames.push_back(filename); outputTypes["list"].push_back(filename);
- m->openOutputFile(filename, *temp);
- }
-
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
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();
- 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;
+ delete list; if (groupfile != "") { delete groupMap; }
+ 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;
- for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
+ delete list; if (groupfile != "") { delete groupMap; }
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;
- for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
+ if (groupfile != "") { delete groupMap; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
}
if (m->control_pressed) {
- delete input; delete groupMap;
- for (i=0; i<gGroups.size(); i++) { (*(filehandles[gGroups[i]])).close(); delete filehandles[gGroups[i]]; }
+ if (groupfile != "") { delete groupMap; }
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 list;
}
- for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
- (*(filehandles[it3->first])).close();
- 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();
/**********************************************************************************************************************/
int ParseListCommand::parse(ListVector* thisList) {
try {
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ //set fileroot
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = thisList->getLabel();
+
+ //fill filehandles with neccessary ofstreams
+ ofstream* temp;
+ vector<string> gGroups;
+ if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); }
+ else { gGroups = ct.getNamesOfGroups(); }
+
+ for (int i=0; i<gGroups.size(); i++) {
+ temp = new ofstream;
+ filehandles[gGroups[i]] = temp;
+
+ variables["[group]"] = gGroups[i];
+ string filename = getOutputFileName("list",variables);
+ m->openOutputFile(filename, *temp);
+ outputNames.push_back(filename); outputTypes["list"].push_back(filename);
+ }
+
map<string, string> groupVector;
+ map<string, string> groupLabels;
map<string, string>::iterator itGroup;
map<string, int> groupNumBins;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
groupNumBins[it3->first] = 0;
groupVector[it3->first] = "";
+ groupLabels[it3->first] = "label\tnumOtus\t";
}
-
+ vector<string> binLabels = thisList->getLabels();
for (int i = 0; i < thisList->getNumBins(); i++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { break; }
map<string, string> groupBins;
string bin = list->get(i);
//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
for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
- groupVector[itGroup->first] += itGroup->second + '\t';
+ groupVector[itGroup->first] += itGroup->second + '\t';
+ groupLabels[itGroup->first] += binLabels[i] + '\t';
}
}
+ if (m->control_pressed) {
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ delete it3->second;
+ }
+ return 0;
+ }
+
//end list vector
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])) << groupLabels[it3->first] << endl;
(*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl; // label numBins listvector for that group
+ (*(filehandles[it3->first])).close();
+ delete it3->second;
}
return 0;
projects / mothur.git / blobdiff