From: westcott <westcott>
Date: Fri, 17 Dec 2010 18:54:42 +0000 (+0000)
Subject: added design parameter to the indicator command
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=0746c58a680458c0bc874b3a5fc1334b12ed2f18;p=mothur.git
added design parameter to the indicator command
---
diff --git a/groupmap.cpp b/groupmap.cpp
index f6705e5..9e99556 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -161,4 +161,25 @@ vector<string> GroupMap::getNamesSeqs(){
}
}
/************************************************************/
+vector<string> GroupMap::getNamesSeqs(vector<string> picked){
+ try {
+
+ vector<string> names;
+
+ for (it = groupmap.begin(); it != groupmap.end(); it++) {
+ //if you are belong to one the the groups in the picked vector add you
+ if (m->inUsersGroups(it->second, picked)) {
+ names.push_back(it->first);
+ }
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "getNamesSeqs");
+ exit(1);
+ }
+}
+
+/************************************************************/
diff --git a/groupmap.h b/groupmap.h
index d0e43c5..54085a1 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -30,6 +30,7 @@ public:
map<string, int> groupIndex; //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
int getNumSeqs() { return groupmap.size(); }
vector<string> getNamesSeqs();
+ vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
int getNumSeqs(string); //return the number of seqs in a given group
private:
diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 01627c0..143135f 100644
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -8,10 +8,12 @@
*/
#include "indicatorcommand.h"
+#include "sharedutilities.h"
+
//**********************************************************************************************************************
vector<string> IndicatorCommand::getValidParameters(){
try {
- string Array[] = {"tree","shared","relabund","label","groups","outputdir","inputdir"};
+ string Array[] = {"tree","shared","relabund","design","label","groups","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
@@ -69,7 +71,7 @@ IndicatorCommand::IndicatorCommand(string option) {
else {
//valid paramters for this command
- string Array[] = {"tree","shared","relabund","groups","label","outputdir","inputdir"};
+ string Array[] = {"tree","shared","design","relabund","groups","label","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
@@ -118,6 +120,13 @@ IndicatorCommand::IndicatorCommand(string option) {
if (path == "") { parameters["relabund"] = inputDir + it->second; }
}
+ it = parameters.find("design");
+ //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["design"] = inputDir + it->second; }
+ }
}
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
@@ -138,6 +147,10 @@ IndicatorCommand::IndicatorCommand(string option) {
else if (relabundfile == "not found") { relabundfile = ""; }
else { inputFileName = relabundfile; }
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { abort = true; }
+ else if (designfile == "not found") { designfile = ""; }
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; Groups.push_back("all"); }
else { m->splitAtDash(groups, Groups); }
@@ -164,8 +177,9 @@ void IndicatorCommand::help(){
m->mothurOut("The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \n");
m->mothurOut("The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n");
m->mothurOut("The summary file lists the indicator value for each OTU for each node.\n");
- m->mothurOut("The indicator command parameters are tree, groups, shared, relabund and label. The tree parameter is required as well as either shared or relabund.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed. The groups may be entered separated by dashes.\n");
+ m->mothurOut("The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n");
+ m->mothurOut("The design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file. The groups may be entered separated by dashes.\n");
m->mothurOut("The label parameter indicates at what distance your tree relates to the shared or relabund.\n");
m->mothurOut("The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
@@ -187,18 +201,35 @@ int IndicatorCommand::execute(){
if (abort == true) { return 0; }
+ //read designfile if given and set up globaldatas groups for read of sharedfiles
+ if (designfile != "") {
+ designMap = new GroupMap(designfile);
+ designMap->readDesignMap();
+
+ //fill Groups - checks for "all" and for any typo groups
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Groups, designMap->namesOfGroups);
+ delete util;
+
+ //loop through the Groups and fill Globaldata's Groups with the design file info
+ globaldata->Groups = designMap->getNamesSeqs(Groups);
+ }
+
/***************************************************/
// use smart distancing to get right sharedRabund //
/***************************************************/
if (sharedfile != "") {
getShared();
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+ if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
}else {
getSharedFloat();
- if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+ if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
}
+
+ //reset Globaldatas groups if needed
+ if (designfile != "") { globaldata->Groups = Groups; }
/***************************************************/
// reading tree info //
@@ -209,16 +240,33 @@ int IndicatorCommand::execute(){
globaldata->setGroupFile(groupfile);
treeMap = new TreeMap();
bool mismatch = false;
+
for (int i = 0; i < globaldata->Treenames.size(); i++) {
//sanity check - is this a group that is not in the sharedfile?
- if (!(m->inUsersGroups(globaldata->Treenames[i], globaldata->gGroupmap->namesOfGroups))) {
- m->mothurOut("[ERROR]: " + globaldata->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
- mismatch = true;
+ if (designfile == "") {
+ if (!(m->inUsersGroups(globaldata->Treenames[i], globaldata->gGroupmap->namesOfGroups))) {
+ m->mothurOut("[ERROR]: " + globaldata->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
+ mismatch = true;
+ }
+ treeMap->addSeq(globaldata->Treenames[i], "Group1");
+ }else{
+ vector<string> myGroups; myGroups.push_back(globaldata->Treenames[i]);
+ vector<string> myNames = designMap->getNamesSeqs(myGroups);
+
+ for(int k = 0; k < myNames.size(); k++) {
+ if (!(m->inUsersGroups(myNames[k], globaldata->gGroupmap->namesOfGroups))) {
+ m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
+ mismatch = true;
+ }
+ }
+ treeMap->addSeq(globaldata->Treenames[i], "Group1");
}
- treeMap->addSeq(globaldata->Treenames[i], "Group1");
}
+
+ if ((designfile != "") && (globaldata->Treenames.size() != Groups.size())) { m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
if (mismatch) { //cleanup and exit
+ if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
delete treeMap;
@@ -236,7 +284,8 @@ int IndicatorCommand::execute(){
delete read;
- if (m->control_pressed) {
+ if (m->control_pressed) {
+ if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
for (int i = 0; i < T.size(); i++) { delete T[i]; } globaldata->gTree.clear(); delete globaldata->gTreemap; return 0;
@@ -256,7 +305,8 @@ int IndicatorCommand::execute(){
for (int i = 0; i < T.size(); i++) { delete T[i]; } globaldata->gTree.clear();
- if (m->control_pressed) {
+ if (m->control_pressed) {
+ if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
delete outputTree; delete globaldata->gTreemap; return 0;
@@ -267,6 +317,8 @@ int IndicatorCommand::execute(){
/***************************************************/
GetIndicatorSpecies(outputTree);
+ if (designfile != "") { delete designMap; }
+
if (m->control_pressed) {
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
@@ -301,7 +353,16 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
+
+ int numBins = 0;
+ if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
+ else { numBins = lookupFloat[0]->getNumBins(); }
+
+ //print headings
+ out << "TreeNode\t";
+ for (int i = 0; i < numBins; i++) { out << "OTU-" << (i+1) << '\t'; }
+ out << endl;
+
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
@@ -379,10 +440,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
}
if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
- //for (int k = 0; k < lookup.size(); k++) {
- // if (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0) { cout << lookup[k]->getGroup() << endl; }
- //}
-
+
indicatorValues = getValues(groupings);
}else {
@@ -651,8 +709,18 @@ set<string> IndicatorCommand::getDescendantList(Tree*& T, int i, map<int, set<st
if (lc == -1) { //you are a leaf your only descendant is yourself
set<int> temp; temp.insert(i);
- names.insert(T->tree[i].getName());
nodes[i] = temp;
+
+ if (designfile == "") {
+ names.insert(T->tree[i].getName());
+ }else {
+ vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
+ vector<string> myReps = designMap->getNamesSeqs(myGroup);
+ for (int k = 0; k < myReps.size(); k++) {
+ names.insert(myReps[k]);
+ }
+ }
+
}else{ //your descedants are the combination of your childrens descendants
names = descendants[lc];
nodes[i] = nodes[lc];
diff --git a/indicatorcommand.h b/indicatorcommand.h
index 0ec100a..ae74997 100644
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -34,7 +34,8 @@ private:
GlobalData* globaldata;
ReadTree* read;
TreeMap* treeMap;
- string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
+ GroupMap* designMap;
+ string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
bool abort;
vector<string> outputNames, Groups;
map<string, vector<string> > outputTypes;
diff --git a/mothur b/mothur
index dfbb7ad..f7fdc10 100755
Binary files a/mothur and b/mothur differ
diff --git a/tree.cpp b/tree.cpp
index c67f03d..08ee850 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -401,7 +401,7 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
int nextSpot = numLeaves;
populateNewTree(copy->tree, root, nextSpot);
-
+
}
catch(exception& e) {
m->errorOut(e, "Tree", "getCopy");