changed get.sharedotu to get.sharedseqs

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ed1801a8bd58bb46fc9afc5e714072547ae4305f..c85326854b1253710f8f56e7bcacf37290cc1ed5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -113,7 +113,7 @@ CommandFactory::CommandFactory(){
        commands["remove.seqs"]                 = "get.seqs";
        commands["system"]                              = "system";
        commands["align.check"]                 = "align.check";
-       commands["get.sharedotu"]               = "get.sharedotu";
+       commands["get.sharedseqs"]              = "get.sharedseqs";
        commands["get.listcount"]               = "get.listcount";
        commands["quit"]                                = "quit"; 
        commands["hcluster"]                    = "hcluster"; 
@@ -181,7 +181,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                   }
                else if(commandName == "system")                                {       command = new SystemCommand(optionString);                              }
                else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                  }
-               else if(commandName == "get.sharedotu")                 {       command = new GetSharedOTUCommand(optionString);                }
+               else if(commandName == "get.sharedseqs")                        {       command = new GetSharedOTUCommand(optionString);                }
                else if(commandName == "get.listcount")                 {       command = new GetListCountCommand(optionString);                }
                else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
                else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                }

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 6d134728899b2a0b127be542e3f26547022d0fb3..76e5725d850e17d52bff0c72abfd2d83669778ee 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -84,15 +84,15 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option){
 
 void GetSharedOTUCommand::help(){
        try {
-               mothurOut("The get.sharedotu command parameters are list, group, label, groups, output and fasta.  The list and group parameters are required.\n");
+               mothurOut("The get.sharedseqs command parameters are list, group, label, groups, output and fasta.  The list and group parameters are required.\n");
                mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
                mothurOut("The groups parameter allows you to select groups you would like to know the shared info for, and are separated by dashes.\n");
                mothurOut("The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n");
                mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n");
                mothurOut("With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n");
-               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 get.sharedseqs 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.sharedseqs command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
+               mothurOut("Example get.sharedseqs(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");
@@ -224,7 +224,12 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                map<string, string> fastaMap;
                
                ofstream outNames;
-               string outputFileNames = getRootName(listfile) + shared->getLabel() + ".names";
+               string outputFileNames;
+               if (output != "accnos") {
+                       outputFileNames = getRootName(listfile) + shared->getLabel() + ".shared.seqs";
+               }else {
+                       outputFileNames = getRootName(listfile) + shared->getLabel() + ".accnos";
+               }
                openOutputFile(outputFileNames, outNames);
                
                bool wroteSomething = false;
@@ -250,7 +255,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                                //find group
                                string seqGroup = groupMap->getGroup(name);
                                if (output != "accnos") {
-                                       namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
+                                       namesOfSeqsInThisBin.push_back((name + "\t" + seqGroup + "\t" + toString(i+1)));
                                }else {  namesOfSeqsInThisBin.push_back(name);  }
 
                                if (seqGroup == "not found") { mothurOut(name + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1);  }
@@ -266,7 +271,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                        if (sharedByAll) {
                                string seqGroup = groupMap->getGroup(names);
                                if (output != "accnos") {
-                                       namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
+                                       namesOfSeqsInThisBin.push_back((names + "\t" + seqGroup + "\t" + toString(i+1)));
                                }else {  namesOfSeqsInThisBin.push_back(names); }
                                
                                if (seqGroup == "not found") { mothurOut(names + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1);  }
@@ -295,8 +300,8 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                                        
                                        if (fastafile != "") { 
                                                if (output != "accnos") {
-                                                       string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
-                                                       seqName = seqName.substr(0,seqName.find_last_of('|'));
+                                                       string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('\t'));
+                                                       seqName = seqName.substr(0,seqName.find_last_of('\t'));
                                                        fastaMap[seqName] = namesOfSeqsInThisBin[j];  //fastaMap needs to contain just the seq name for output later
                                                }else {
                                                        fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
@@ -326,7 +331,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                
                //if fasta file provided output new fasta file
                if ((fastafile != "") && wroteSomething) {      
-                       string outputFileFasta = getRootName(fastafile) + shared->getLabel() + ".fasta";
+                       string outputFileFasta = getRootName(fastafile) + shared->getLabel() + ".shared.fasta";
                        ofstream outFasta;
                        openOutputFile(outputFileFasta, outFasta);