try {
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
+ //CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
helpString += "The make.shared command parameters are list, group, ordergroup, groups and label. list and group are required unless a current file is available.\n";
helpString += "The groups parameter allows you to indicate which groups you want to include, group names should be separated by dashes. ex. groups=A-B-C. Default is all groups in your groupfile.\n";
helpString += "The label parameter allows you to indicate which labels you want to include, label names should be separated by dashes. Default is all labels in your list file.\n";
- helpString += "The ordergroup parameter allows you to indicate the order of the groups in the sharedfile, by default the groups are listed alphabetically.\n";
+ //helpString += "The ordergroup parameter allows you to indicate the order of the groups in the sharedfile, by default the groups are listed alphabetically.\n";
return helpString;
}
catch(exception& e) {
int error = groupMap->readMap();
if (error == 1) { abort = true; }
- m->namesOfGroups = groupMap->namesOfGroups;
+ vector<string> allGroups = groupMap->getNamesOfGroups();
+ m->setAllGroups(allGroups);
}
else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
}else {
int error = groupMap->readMap();
if (error == 1) { abort = true; }
- m->namesOfGroups = groupMap->namesOfGroups;
+ vector<string> allGroups = groupMap->getNamesOfGroups();
+ m->setAllGroups(allGroups);
m->setGroupFile(groupfile);
}
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
//check for optional parameter and set defaults
//if hte user has not specified any groups then use them all
if (Groups.size() == 0) {
- Groups = groupMap->namesOfGroups; m->Groups = Groups;
+ Groups = groupMap->getNamesOfGroups(); m->setGroups(Groups);
}else { pickedGroups = true; }
//fill filehandles with neccessary ofstreams
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
-
- if ((m->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
+
+ //sanity check
+ int error = ListGroupSameSeqs();
+
+ if ((!pickedGroups) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
out.close();
return 0;
}
+ if (error == 1) { m->control_pressed = true; }
+
//if user has specified groups make new groupfile for them
if (pickedGroups) { //make new group file
string groups = "";
- if (m->Groups.size() < 4) {
- for (int i = 0; i < m->Groups.size(); i++) {
- groups += m->Groups[i] + ".";
+ if (m->getNumGroups() < 4) {
+ for (int i = 0; i < m->getNumGroups(); i++) {
+ groups += (m->getGroups())[i] + ".";
}
}else { groups = "merge"; }
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
- if (isValidGroup(groupName, m->Groups)) {
+ if (isValidGroup(groupName, m->getGroups())) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
if (order.size() == 0) { //user has not specified an order so do aplabetically
sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
- m->Groups.clear();
+ m->clearGroups();
+ vector<string> Groups;
//initialize bin values
for (int i = 0; i < thislookup.size(); i++) {
out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
thislookup[i]->print(out);
- m->Groups.push_back(thislookup[i]->getGroup());
+ Groups.push_back(thislookup[i]->getGroup());
RAbundVector rav = thislookup[i]->getRAbundVector();
m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
rav.print(*(filehandles[thislookup[i]->getGroup()]));
(*(filehandles[thislookup[i]->getGroup()])).close();
}
+ m->setGroups(Groups);
}else{
//create a map from groupName to each sharedrabund
map<string, SharedRAbundVector*> myMap;
myMap[thislookup[i]->getGroup()] = thislookup[i];
}
- m->Groups.clear();
+ m->clearGroups();
+ vector<string> Groups;
//loop through ordered list and print the rabund
for (int i = 0; i < order.size(); i++) {
out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
(myIt->second)->print(out);
- m->Groups.push_back((myIt->second)->getGroup());
+ Groups.push_back((myIt->second)->getGroup());
RAbundVector rav = (myIt->second)->getRAbundVector();
m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
}
}
+
+ m->setGroups(Groups);
}
exit(1);
}
}
-
+//**********************************************************************************************************************
+int SharedCommand::ListGroupSameSeqs() {
+ try {
+
+ int error = 0;
+
+ vector<string> groupMapsSeqs = groupMap->getNamesSeqs();
+
+ set<string> groupNamesSeqs;
+ for(int i = 0; i < groupMapsSeqs.size(); i++) {
+ groupNamesSeqs.insert(groupMapsSeqs[i]);
+ }
+
+
+ //go through list and if group returns "not found" output it
+ for (int i = 0; i < SharedList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ string names = SharedList->get(i);
+
+ vector<string> listNames;
+ m->splitAtComma(names, listNames);
+
+ for (int j = 0; j < listNames.size(); j++) {
+ int num = groupNamesSeqs.count(listNames[j]);
+
+ if (num == 0) { error = 1; m->mothurOut("[ERROR]: " + listNames[j] + " is in your listfile and not in your groupfile. Please correct."); m->mothurOutEndLine(); }
+ else { groupNamesSeqs.erase(listNames[j]); }
+ }
+ }
+
+ for (set<string>::iterator itGroupSet = groupNamesSeqs.begin(); itGroupSet != groupNamesSeqs.end(); itGroupSet++) {
+ error = 1;
+ m->mothurOut("[ERROR]: " + (*itGroupSet) + " is in your groupfile and not your listfile. Please correct."); m->mothurOutEndLine();
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "ListGroupSameSeqs");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SharedCommand::~SharedCommand(){
projects / mothur.git / blobdiff