if (itGroup != g.end()) {
groupCounts[indexGroupMap[itGroup->second]] = 1;
totalGroups[indexGroupMap[itGroup->second]]++;
- }else { m->mothurOut("[ERROR]: Your group file does not contain " + seqName + ". Please correct."); m->mothurOutEndLine(); }
+ }else {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ m->mothurOut("[ERROR]: Your group file does not contain " + seqName + ". Please correct."); m->mothurOutEndLine();
+ }
map<string, int>::iterator it2 = indexNameMap.find(seqName);
if (it2 == indexNameMap.end()) {
}
}
+ if (hasGroups) {
+ for (int i = 0; i < totalGroups.size(); i++) {
+ if (totalGroups[i] == 0) { m->mothurOut("\nRemoving group: " + groups[i] + " because all sequences have been removed.\n"); removeGroup(groups[i]); i--; }
+ }
+ }
+
return 0;
}
catch(exception& e) {
string firstCol, secondCol;
in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in);
+ m->checkName(firstCol);
+ m->checkName(secondCol);
+
vector<string> names;
m->splitAtChar(secondCol, names, ',');
in.close();
if (error) { m->control_pressed = true; }
- if (groupfile != "") { delete groupMap; }
+ else { //check for zero groups
+ if (hasGroups) {
+ for (int i = 0; i < totalGroups.size(); i++) {
+ if (totalGroups[i] == 0) { m->mothurOut("\nRemoving group: " + groups[i] + " because all sequences have been removed.\n"); removeGroup(groups[i]); i--; }
+ }
+ }
+ }
+ if (groupfile != "") { delete groupMap; }
return 0;
}
}
}
/************************************************************/
-int CountTable::readTable(string file) {
+int CountTable::readTable(string file, bool readGroups) {
try {
filename = file;
ifstream in;
indexNameMap.clear();
counts.clear();
map<int, string> originalGroupIndexes;
- if (columnHeaders.size() > 2) { hasGroups = true; numGroups = columnHeaders.size() - 2; }
+ if ((columnHeaders.size() > 2) && readGroups) { hasGroups = true; numGroups = columnHeaders.size() - 2; }
for (int i = 2; i < columnHeaders.size(); i++) { groups.push_back(columnHeaders[i]); originalGroupIndexes[i-2] = columnHeaders[i]; totalGroups.push_back(0); }
//sort groups to keep consistent with how we store the groups in groupmap
sort(groups.begin(), groups.end());
//if group info, then read it
vector<int> groupCounts; groupCounts.resize(numGroups, 0);
- for (int i = 0; i < numGroups; i++) { int thisIndex = indexGroupMap[originalGroupIndexes[i]]; in >> groupCounts[thisIndex]; m->gobble(in); totalGroups[thisIndex] += groupCounts[thisIndex]; }
+ if (columnHeaders.size() > 2) { //file contains groups
+ if (readGroups) { //user wants to save them
+ for (int i = 0; i < numGroups; i++) { int thisIndex = indexGroupMap[originalGroupIndexes[i]]; in >> groupCounts[thisIndex]; m->gobble(in); totalGroups[thisIndex] += groupCounts[thisIndex]; }
+ }else { //read and discard
+ m->getline(in); m->gobble(in);
+ }
+ }
map<string, int>::iterator it = indexNameMap.find(name);
if (it == indexNameMap.end()) {
in.close();
if (error) { m->control_pressed = true; }
+ else { //check for zero groups
+ if (hasGroups) {
+ for (int i = 0; i < totalGroups.size(); i++) {
+ if (totalGroups[i] == 0) { m->mothurOut("\nRemoving group: " + groups[i] + " because all sequences have been removed.\n"); removeGroup(groups[i]); i--; }
+ }
+ }
+ }
return 0;
}
for (int i = 0; i < groups.size(); i++) { out << groups[i] << '\t'; }
out << endl;
- for (map<string, int>::iterator itNames = indexNameMap.begin(); itNames != indexNameMap.end(); itNames++) {
+ map<int, string> reverse; //use this to preserve order
+ for (map<string, int>::iterator it = indexNameMap.begin(); it !=indexNameMap.end(); it++) { reverse[it->second] = it->first; }
+
+ for (int i = 0; i < totals.size(); i++) {
+ map<int, string>::iterator itR = reverse.find(i);
+
+ if (itR != reverse.end()) { //will equal end if seqs were removed because remove just removes from indexNameMap
+ out << itR->second << '\t' << totals[i] << '\t';
+ if (hasGroups) {
+ for (int j = 0; j < groups.size(); j++) {
+ out << counts[i][j] << '\t';
+ }
+ }
+ out << endl;
+ }
+ }
+ /*for (map<string, int>::iterator itNames = indexNameMap.begin(); itNames != indexNameMap.end(); itNames++) {
out << itNames->first << '\t' << totals[itNames->second] << '\t';
if (hasGroups) {
}
}
out << endl;
- }
+ }*/
out.close();
return 0;
}
if (hasGroups) {
map<string, int>::iterator it = indexNameMap.find(seqName);
if (it == indexNameMap.end()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
temp = counts[it->second];
if (hasGroups) {
map<string, int>::iterator it = indexGroupMap.find(groupName);
if (it == indexGroupMap.end()) {
- m->mothurOut("[ERROR]: " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+ m->mothurOut("[ERROR]: group " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
return totalGroups[it->second];
}
if (hasGroups) {
map<string, int>::iterator it = indexGroupMap.find(groupName);
if (it == indexGroupMap.end()) {
- m->mothurOut("[ERROR]: " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+ m->mothurOut("[ERROR]: group " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
map<string, int>::iterator it2 = indexNameMap.find(seqName);
if (it2 == indexNameMap.end()) {
- m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ m->mothurOut("[ERROR]: seq " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
return counts[it2->second][it->second];
}
}else {
map<string, int>::iterator it2 = indexNameMap.find(seqName);
if (it2 == indexNameMap.end()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
int oldCount = counts[it2->second][it->second];
}
}
/************************************************************/
+//remove group
+int CountTable::removeGroup(string groupName) {
+ try {
+ if (hasGroups) {
+ //save for later in case removing a group means we need to remove a seq.
+ map<int, string> reverse;
+ for (map<string, int>::iterator it = indexNameMap.begin(); it !=indexNameMap.end(); it++) { reverse[it->second] = it->first; }
+
+ map<string, int>::iterator it = indexGroupMap.find(groupName);
+ if (it == indexGroupMap.end()) {
+ m->mothurOut("[ERROR]: " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+ }else {
+ int indexOfGroupToRemove = it->second;
+ map<string, int> currentGroupIndex = indexGroupMap;
+ vector<string> newGroups;
+ for (int i = 0; i < groups.size(); i++) {
+ if (groups[i] != groupName) {
+ newGroups.push_back(groups[i]);
+ indexGroupMap[groups[i]] = newGroups.size()-1;
+ }
+ }
+ indexGroupMap.erase(groupName);
+ groups = newGroups;
+ totalGroups.erase(totalGroups.begin()+indexOfGroupToRemove);
+
+ int thisIndex = 0;
+ map<string, int> newIndexNameMap;
+ for (int i = 0; i < counts.size(); i++) {
+ int num = counts[i][indexOfGroupToRemove];
+ counts[i].erase(counts[i].begin()+indexOfGroupToRemove);
+ totals[i] -= num;
+ total -= num;
+ if (totals[i] == 0) { //your sequences are only from the group we want to remove, then remove you.
+ counts.erase(counts.begin()+i);
+ totals.erase(totals.begin()+i);
+ uniques--;
+ i--;
+ }
+ newIndexNameMap[reverse[thisIndex]] = i;
+ thisIndex++;
+ }
+ indexNameMap = newIndexNameMap;
+
+ if (groups.size() == 0) { hasGroups = false; }
+ }
+ }else { m->mothurOut("[ERROR]: your count table does not contain group information, can not remove group " + groupName + ".\n"); m->control_pressed = true; }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountTable", "removeGroup");
+ exit(1);
+ }
+}
+/************************************************************/
//vector of groups for the seq
vector<string> CountTable::getGroups(string seqName) {
try {
map<string, int>::iterator it = indexNameMap.find(oldSeqName);
if (it == indexNameMap.end()) {
+ if (hasGroupInfo()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(oldSeqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + oldSeqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ }
m->mothurOut("[ERROR]: " + oldSeqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
int index = it->second;
map<string, int>::iterator it = indexNameMap.find(seqName);
if (it == indexNameMap.end()) {
+ if (hasGroupInfo()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ }
m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
return totals[it->second];
map<string, int>::iterator it = indexNameMap.find(seqName);
if (it == indexNameMap.end()) {
+ if (hasGroupInfo()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ }
m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else { return it->second; }
int CountTable::remove(string seqName) {
try {
map<string, int>::iterator it = indexNameMap.find(seqName);
- if (it == indexNameMap.end()) {
+ if (it != indexNameMap.end()) {
uniques--;
if (hasGroups){ //remove this sequences counts from group totals
for (int i = 0; i < totalGroups.size(); i++) { totalGroups[i] -= counts[it->second][i]; counts[it->second][i] = 0; }
total -= thisTotal;
indexNameMap.erase(it);
}else {
+ if (hasGroupInfo()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seqName, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ }
m->mothurOut("[ERROR]: Your count table contains does not include " + seqName + ", cannot remove."); m->mothurOutEndLine(); m->control_pressed = true;
}
}
}
/************************************************************/
+//returns the names of all unique sequences in file mapped to their seqCounts
+map<string, int> CountTable::getNameMap() {
+ try {
+ map<string, int> names;
+ for (map<string, int>::iterator it = indexNameMap.begin(); it != indexNameMap.end(); it++) {
+ names[it->first] = totals[it->second];
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountTable", "getNameMap");
+ exit(1);
+ }
+}
+/************************************************************/
//returns the names of all unique sequences in file
vector<string> CountTable::getNamesOfSeqs(string group) {
try {
try {
map<string, int>::iterator it = indexNameMap.find(seq1);
if (it == indexNameMap.end()) {
+ if (hasGroupInfo()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seq1, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seq1 + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ }
m->mothurOut("[ERROR]: " + seq1 + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
map<string, int>::iterator it2 = indexNameMap.find(seq2);
if (it2 == indexNameMap.end()) {
+ if (hasGroupInfo()) {
+ //look for it in names of groups to see if the user accidently used the wrong file
+ if (m->inUsersGroups(seq2, groups)) {
+ m->mothurOut("[WARNING]: Your group or design file contains a group named " + seq2 + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+ }
+ }
m->mothurOut("[ERROR]: " + seq2 + " is not in your count table. Please correct.\n"); m->control_pressed = true;
}else {
//merge data
projects / mothur.git / blobdiff