changed how we break up the files on parallelized commands to avoid scanning file.

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index c4bf523fb30be6f1bd84dc81eac85e3e92c9e6f8..5b9cde8c84b10e0d4f6dd938dbf68191000930f4 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -21,7 +21,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"list","order","shared", "label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
+                       string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -97,7 +97,14 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
                                }
-
+                               
+                               it = parameters.find("relabund");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
+                               }
                        }
 
                        
@@ -130,6 +137,12 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        else if (sharedfile == "not found") { sharedfile = ""; }
                        else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
                        
+                       relAbundfile = validParameter.validFile(parameters, "relabund", true);
+                       if (relAbundfile == "not open") { abort = true; }       
+                       else if (relAbundfile == "not found") { relAbundfile = ""; }
+                       else {  globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund");   }
+
+                       
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
@@ -154,8 +167,8 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
                        
                        //you have not given a file
-                       if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
-                               m->mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true; 
+                       if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) {
+                               m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true; 
                        }
                
                        //check for optional parameter and set defaults
@@ -194,7 +207,7 @@ void ReadOtuCommand::help(){
        try {
                m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
                m->mothurOut("collect.shared, rarefaction.shared, summary.shared heatmap.bin, heatmap.sim or venn command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
-               m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, ordergroup, label and groups.\n");
+               m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, relabund, group, order, ordergroup, label and groups.\n");
                m->mothurOut("The read.otu command can be used in two ways.  The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n");
                m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
                m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");