working on pam

[mothur.git] / makelefsecommand.cpp

diff --git a/makelefsecommand.cpp b/makelefsecommand.cpp
index 8f2857e5e302b0587555a03e6a705082c47f9d45..c859bfbc230201e4be1ef73ab19ed56f28b3412d 100644 (file)
--- a/makelefsecommand.cpp
+++ b/makelefsecommand.cpp
@@ -7,6 +7,7 @@
 //
 
 #include "makelefsecommand.h"
+#include "designmap.h"
 
 //**********************************************************************************************************************
 vector<string> MakeLefseCommand::setParameters(){
@@ -42,8 +43,8 @@ string MakeLefseCommand::getHelpString(){
         helpString += "The constaxonomy parameter is used to input your taxonomy file. http://www.wiki.mothur.org/wiki/Constaxonomy_file. The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance.  ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled. \n";
         helpString += "The scale parameter allows you to select what scale you would like to use to convert your shared file abundances to relative abundances. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n";
                helpString += "The label parameter allows you to select what distance level you would like used, if none is given the first distance is used.\n";
-               helpString += "The make.lefse command should be in the following format: make.lefse(list=yourListFile, taxonomy=outputFromClassify.seqsCommand, name=yourNameFile)\n";
-               helpString += "make.lefse(shared=final.an.list, taxonomy=final.an.taxonomy, name=final.names)\n";
+               helpString += "The make.lefse command should be in the following format: make.lefse(shared=yourSharedFile)\n";
+               helpString += "make.lefse(shared=final.an.shared)\n";
                return helpString;
        }
        catch(exception& e) {
@@ -258,28 +259,37 @@ int MakeLefseCommand::runRelabund(map<string, consTax2>& consTax, vector<SharedR
         ofstream out;
         m->openOutputFile(outputFile, out);
 
-        GroupMap* designMap = NULL;
+        DesignMap* designMap = NULL;
         if (designfile != "") {
-            designMap = new GroupMap(designfile);
-            designMap->readDesignMap();
+            designMap = new DesignMap(designfile);
+            vector<string> categories = designMap->getNamesOfCategories();
             
-            out << "treatment\t";
-            for (int i = 0; i < lookup.size(); i++) {
-                string treatment = designMap->getGroup(lookup[i]->getGroup());
-                if (treatment == "not found") {
-                    m->mothurOut("[ERROR]: " + lookup[i]->getGroup() + " is not in your design file, please correct.\n"); 
-                }else { out << treatment << '\t'; }
+            if (categories.size() > 3) {  m->mothurOut("\n[NOTE]: LEfSe input files allow for a class, subclass and subject.  More than 3 categories can cause formatting errors.\n\n"); }
+            
+            for (int j = 0; j < categories.size(); j++) {
+                out << categories[j] << "\t";
+                for (int i = 0; i < lookup.size()-1; i++) {
+                    if (m->control_pressed) { out.close(); delete designMap; return 0; }
+                    string value = designMap->get(lookup[i]->getGroup(), categories[j]);
+                    if (value == "not found") {
+                        m->mothurOut("[ERROR]: " + lookup[i]->getGroup() + " is not in your design file, please correct.\n"); m->control_pressed = true;
+                    }else { out << value << '\t'; }
+                }
+                string value = designMap->get(lookup[lookup.size()-1]->getGroup(), categories[j]);
+                if (value == "not found") {
+                    m->mothurOut("[ERROR]: " + lookup[lookup.size()-1]->getGroup() + " is not in your design file, please correct.\n"); m->control_pressed = true;
+                }else { out << value; }
+                out << endl;
             }
-            out << endl;
         }
         
         out << "group\t";
-        for (int i = 0; i < lookup.size(); i++) {  out << lookup[i]->getGroup() << '\t'; }
-        out << endl;
+        for (int i = 0; i < lookup.size()-1; i++) {  out << lookup[i]->getGroup() << '\t'; }
+        out << lookup[lookup.size()-1]->getGroup() << endl;
         
         for (int i = 0; i < lookup[0]->getNumBins(); i++) { //process each otu
             if (m->control_pressed) { break; }
-            string nameOfOtu = m->currentBinLabels[i];
+            string nameOfOtu = m->currentSharedBinLabels[i];
             if (constaxonomyfile != "") { //try to find the otuName in consTax to replace with consensus taxonomy
                 map<string, consTax2>::iterator it = consTax.find(nameOfOtu);
                 if (it != consTax.end()) {
@@ -289,7 +299,7 @@ int MakeLefseCommand::runRelabund(map<string, consTax2>& consTax, vector<SharedR
                     //remove confidences and change ; to |
                     m->removeConfidences(nameOfOtu);
                     for (int j = 0; j < nameOfOtu.length()-1; j++) {
-                        if (nameOfOtu[j] == ';') { fixedName += "_" + m->currentBinLabels[i] + '|'; }
+                        if (nameOfOtu[j] == ';') { fixedName += "_" + m->currentSharedBinLabels[i] + '|'; }
                         else { fixedName += nameOfOtu[j]; }
                     }
                     nameOfOtu = fixedName;
@@ -302,8 +312,9 @@ int MakeLefseCommand::runRelabund(map<string, consTax2>& consTax, vector<SharedR
             out << nameOfOtu << '\t';
             
             //print out relabunds for each otu
-            for (int j = 0; j < lookup.size(); j++) { out << lookup[j]->getAbundance(i) << '\t'; }
-            out << endl;
+            for (int j = 0; j < lookup.size()-1; j++) { out << lookup[j]->getAbundance(i) << '\t'; }
+            
+            out << lookup[lookup.size()-1]->getAbundance(i)<< endl;
         }
         out.close();