From: westcott <westcott>
Date: Tue, 9 Nov 2010 17:40:05 +0000 (+0000)
Subject: parsimony calculator changed order of groups to reflect change in shared Utils made...
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=4ad32478c7b1bbb464c839a6e133f5b517a3efec;p=mothur.git
parsimony calculator changed order of groups to reflect change in shared Utils made to make output of summary.shared match unifrac commands
---
diff --git a/fastamap.cpp b/fastamap.cpp
index 25860e1..bf55493 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -64,11 +64,13 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
m->openInputFile(oldNameFileName, oldNameFile);
map<string,string> oldNameMap;
+ map<string, string>::iterator itName;
string name, list;
while(!oldNameFile.eof()){
if (m->control_pressed) { break; }
- oldNameFile >> name >> list;
+ oldNameFile >> name; m->gobble(oldNameFile);
+ oldNameFile >> list;
oldNameMap[name] = list;
m->gobble(oldNameFile);
}
@@ -87,6 +89,10 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
else { sequence = currSeq.getUnaligned(); }
+ itName = seqmap.find(name);
+ if (itName == seqmap.end()) { seqmap[name] = sequence; }
+ else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
seqmap[name] = sequence;
map<string,group>::iterator it = data.find(sequence);
if (it == data.end()) { //it's unique.
diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index b4b4674..1488cda 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -367,7 +367,7 @@ int ListSeqsCommand::readGroup(){
if (m->control_pressed) { in.close(); return 0; }
- in >> name; //read from first column
+ in >> name; m->gobble(in); //read from first column
in >> group; //read from second column
names.push_back(name);
diff --git a/mothur b/mothur
index e33ddcd..1b53d19 100755
Binary files a/mothur and b/mothur differ
diff --git a/mothurout.cpp b/mothurout.cpp
index 9ec847c..bd1a098 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -522,7 +522,7 @@ string MothurOut::getFullPathName(string fileName){
newFileName = homeDir + fileName.substr(fileName.find("~")+1);
return newFileName;
}else { //find path
- if (path.rfind("./") == -1) { return fileName; } //already complete name
+ if (path.rfind("./") == string::npos) { return fileName; } //already complete name
else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
//char* cwdpath = new char[1024];
@@ -542,7 +542,7 @@ string MothurOut::getFullPathName(string fileName){
//break apart the current working directory
vector<string> dirs;
- while (simpleCWD.find_first_of('/') != -1) {
+ while (simpleCWD.find_first_of('/') != string::npos) {
string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
dirs.push_back(dir);
@@ -553,7 +553,7 @@ string MothurOut::getFullPathName(string fileName){
int index = dirs.size()-1;
- while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+ while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
if (pos == 0) { break; //you are at the end
}else if (path[(pos-1)] == '.') { //you want your parent directory ../
path = path.substr(0, pos-1);
@@ -573,12 +573,12 @@ string MothurOut::getFullPathName(string fileName){
return newFileName;
}
#else
- if (path.find("~") != -1) { //go to home directory
+ if (path.find("~") != string::npos) { //go to home directory
string homeDir = getenv ("HOMEPATH");
newFileName = homeDir + fileName.substr(fileName.find("~")+1);
return newFileName;
}else { //find path
- if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+ if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
char *cwdpath = NULL;
@@ -599,7 +599,7 @@ string MothurOut::getFullPathName(string fileName){
int index = dirs.size()-1;
- while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
+ while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
if (pos == 0) { break; //you are at the end
}else if (path[(pos-1)] == '.') { //you want your parent directory ../
path = path.substr(0, pos-1);
@@ -658,7 +658,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
fileHandle.open(completeFileName.c_str());
if(!fileHandle) {
- mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
+ //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
return 1;
}else {
//check for blank file
diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 59126fb..f0a7abc 100644
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -175,7 +175,7 @@ int ParseFastaQCommand::execute(){
if (qual == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
//sanity check sequence length and number of quality scores match
- if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
if (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
//convert quality scores
diff --git a/parsimony.cpp b/parsimony.cpp
index 0487822..efc7d3a 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -34,7 +34,7 @@ EstOutput Parsimony::getValues(Tree* t) {
int count = 0;
for (int a=0; a<numGroups; a++) {
- for (int l = a+1; l < numGroups; l++) {
+ for (int l = 0; l < a; l++) {
int score = 0;
//groups in this combo
diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 0f4042f..1493ee9 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -29,7 +29,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
//set up groupmap for later.
groupmap = new GroupMap(globaldata->getGroupFile());
- groupmap->readMap();
+ groupmap->readMap();
int hold;
string inputData;
diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 036341f..3def1d1 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -8,6 +8,7 @@
*/
#include "subsamplecommand.h"
+#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> SubSampleCommand::getValidParameters(){
@@ -226,6 +227,9 @@ SubSampleCommand::SubSampleCommand(string option) {
if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
+ if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) {
+ m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
+
}
}
@@ -270,10 +274,16 @@ int SubSampleCommand::execute(){
if (abort == true) { return 0; }
if (sharedfile != "") { getSubSampleShared(); }
- //if (listfile != "") { getSubSampleList(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
+ if (listfile != "") { getSubSampleList(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
//if (rabund != "") { getSubSampleRabund(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
//if (sabundfile != "") { getSubSampleSabund(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
//if (fastafile != "") { getSubSampleFasta(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -302,31 +312,31 @@ int SubSampleCommand::getSubSampleShared() {
InputData* input = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
-
+
//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;
-
-
+
+
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { out.close(); return 0; }
-
+ if (m->control_pressed) { delete input; out.close(); return 0; }
+
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
+
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
processShared(lookup, out);
-
+
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
-
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
+
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
@@ -342,14 +352,14 @@ int SubSampleCommand::getSubSampleShared() {
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
-
+
//get next line to process
lookup = input->getSharedRAbundVectors();
}
if (m->control_pressed) { out.close(); return 0; }
-
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
@@ -362,7 +372,7 @@ int SubSampleCommand::getSubSampleShared() {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
-
+
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
@@ -374,11 +384,12 @@ int SubSampleCommand::getSubSampleShared() {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
-
+
+ delete input;
out.close();
-
+
return 0;
-
+
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
@@ -389,7 +400,7 @@ int SubSampleCommand::getSubSampleShared() {
int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofstream& out) {
try {
- if (pickedGroups) { eliminateZeroOTUS(thislookup); }
+ //if (pickedGroups) { eliminateZeroOTUS(thislookup); }
if (size == 0) { //user has not set size, set size = smallest samples size
size = thislookup[0]->getNumSeqs();
@@ -403,11 +414,11 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofs
int numBins = thislookup[0]->getNumBins();
for (int i = 0; i < thislookup.size(); i++) {
int thisSize = thislookup[i]->getNumSeqs();
-
+
if (thisSize != size) {
string thisgroup = thislookup[i]->getGroup();
-
+
OrderVector* order = new OrderVector();
for(int p=0;p<numBins;p++){
for(int j=0;j<thislookup[i]->getAbundance(p);j++){
@@ -425,6 +436,9 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofs
for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { delete order; return 0; }
+
//get random number to sample from order between 0 and thisSize-1.
int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
@@ -440,6 +454,8 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofs
//subsampling may have created some otus with no sequences in them
eliminateZeroOTUS(thislookup);
+ if (m->control_pressed) { return 0; }
+
for (int i = 0; i < thislookup.size(); i++) {
out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
thislookup[i]->print(out);
@@ -449,7 +465,232 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofs
}
catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS");
+ m->errorOut(e, "SubSampleCommand", "processShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SubSampleCommand::getSubSampleList() {
+ try {
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ InputData* input;
+ //if you have a groupfile you want to read a shared list
+ if (groupfile != "") {
+
+ GroupMap* groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Groups, groupMap->namesOfGroups);
+ delete util;
+
+ //create outputfiles
+ string groupOutputDir = outputDir;
+ if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
+ string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
+
+ ofstream outGroup;
+ m->openOutputFile(groupOutputFileName, outGroup);
+ outputTypes["group"].push_back(groupOutputFileName); outputNames.push_back(groupOutputFileName);
+
+ globaldata->setGroupFile(groupfile); //shared list needs this
+
+ input = new InputData(listfile, "list");
+ ListVector* list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ //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;
+
+ //file mismatch quit
+ if (list->getNumSeqs() != groupMap->getNumSeqs()) {
+ m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
+ m->mothurOutEndLine();
+ delete groupMap;
+ delete list;
+ delete input;
+ out.close();
+ outGroup.close();
+ return 0;
+ }
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { delete list; delete input; delete groupMap; out.close(); outGroup.close(); return 0; }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processListGroup(list, groupMap, out, outGroup);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+
+ list = input->getListVector(lastLabel);
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processListGroup(list, groupMap, out, outGroup);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list; list = NULL;
+
+ //get next line to process
+ list = input->getListVector();
+ }
+
+
+ if (m->control_pressed) { if (list != NULL) { delete list; } delete input; delete groupMap; out.close(); outGroup.close(); return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+
+ list = input->getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processListGroup(list, groupMap, out, outGroup);
+
+ delete list; list = NULL;
+ }
+
+ out.close(); outGroup.close();
+ if (list != NULL) { delete list; }
+ delete groupMap;
+
+ }else {
+ //need to complete
+ }
+
+
+ delete input;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getSubSampleList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SubSampleCommand::processListGroup(ListVector*& list, GroupMap*& groupMap, ofstream& out, ofstream& outGroup) {
+ try {
+
+ if (size == 0) { //user has not set size, set size = 10% samples size
+ size = int (list->getNumSeqs() * 0.10);
+ }
+
+ int numBins = list->getNumBins();
+ int thisSize = list->getNumSeqs();
+
+ if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
+ size = thisSize;
+ }
+
+ vector<nameToBin> seqs;
+ for (int i = 0; i < numBins; i++) {
+ string names = list->get(i);
+
+ //parse names
+ string individual = "";
+ int length = names.length();
+ for(int j=0;j<length;j++){
+ if(names[j] == ','){
+ nameToBin temp(individual, i);
+ seqs.push_back(temp);
+ individual = "";
+ }
+ else{
+ individual += names[j];
+ }
+ }
+ nameToBin temp(individual, i);
+ seqs.push_back(temp);
+ }
+
+
+ ListVector* temp = new ListVector(numBins);
+ temp->setLabel(list->getLabel());
+
+ delete list;
+ list = temp;
+
+ set<int> alreadySelected; //dont want repeat sequence names added
+ alreadySelected.insert(-1);
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { return 0; }
+
+ //get random sequence to add, making sure we have not already added it
+ int myrand = -1;
+ while (alreadySelected.count(myrand) != 0) {
+ myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
+ }
+ alreadySelected.insert(myrand);
+
+ //update new list
+ string oldNames = temp->get(seqs[myrand].bin);
+ if (oldNames == "") { oldNames += seqs[myrand].name; }
+ else { oldNames += "," + seqs[myrand].name; }
+
+ temp->set(seqs[myrand].bin, oldNames);
+
+ //update group file
+ string group = groupMap->getGroup(seqs[myrand].name);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + seqs[myrand].name + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+
+ outGroup << seqs[myrand].name << '\t' << group << endl;
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ list->print(out);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "processListGroup");
exit(1);
}
}
diff --git a/subsamplecommand.h b/subsamplecommand.h
index f068ac3..9f3e55b 100644
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -32,6 +32,14 @@ public:
void help();
private:
+
+ struct nameToBin {
+ string name;
+ int bin;
+
+ nameToBin(string n, int b) : name(n), bin(b) {}
+ };
+
GlobalData* globaldata;
bool abort, pickedGroups, allLines;
@@ -44,7 +52,9 @@ private:
int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
int getSubSampleShared();
+ int getSubSampleList();
int processShared(vector<SharedRAbundVector*>&, ofstream&);
+ int processListGroup(ListVector*&, GroupMap*&, ofstream&, ofstream&);
};