added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get...

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 56f030d235212dec72677e15431fef6a6edbcad9..6d134728899b2a0b127be542e3f26547022d0fb3 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -93,6 +93,7 @@ void GetSharedOTUCommand::help(){
                mothurOut("The get.sharedotu command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n");
                mothurOut("The get.sharedotu command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
                mothurOut("Example get.sharedotu(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n");
+               mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n");
                mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
        }
@@ -227,6 +228,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                openOutputFile(outputFileNames, outNames);
                
                bool wroteSomething = false;
+               int num = 0;
                                
                //go through each bin, find out if shared
                for (int i = 0; i < shared->getNumBins(); i++) {
@@ -248,7 +250,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                                //find group
                                string seqGroup = groupMap->getGroup(name);
                                if (output != "accnos") {
-                                       namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i)));
+                                       namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
                                }else {  namesOfSeqsInThisBin.push_back(name);  }
 
                                if (seqGroup == "not found") { mothurOut(name + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1);  }
@@ -264,7 +266,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                        if (sharedByAll) {
                                string seqGroup = groupMap->getGroup(names);
                                if (output != "accnos") {
-                                       namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i)));
+                                       namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
                                }else {  namesOfSeqsInThisBin.push_back(names); }
                                
                                if (seqGroup == "not found") { mothurOut(names + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1);  }
@@ -285,6 +287,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                        if (sharedByAll) {
                                
                                wroteSomething = true;
+                               num++;
                                
                                //output list of names 
                                for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
@@ -310,7 +313,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                
                if (!wroteSomething) {
                        remove(outputFileNames.c_str());
-                       string outputString = " - No otus shared by groups";
+                       string outputString = "\t" + toString(num) + " - No otus shared by groups";
                        
                        string groupString = "";
                        for (int h = 0; h < Groups.size(); h++) {
@@ -319,7 +322,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                        
                        outputString += groupString + ".";
                        mothurOut(outputString); mothurOutEndLine();
-               }else { mothurOutEndLine(); }
+               }else { mothurOut("\t" + toString(num)); mothurOutEndLine(); }
                
                //if fasta file provided output new fasta file
                if ((fastafile != "") && wroteSomething) {