*/
#include "getsharedotucommand.h"
+#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> GetSharedOTUCommand::setParameters(){
helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
- helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
return helpString;
}
catch(exception& e) {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
abort = true;
}
- }else { format = "list"; }
+ }else { format = "list"; m->setListFile(listfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
abort = true;
}
- }
+ }else { m->setGroupFile(groupfile); }
if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
-
+ else { m->setFastaFile(fastafile); }
}
}
userGroups = "unique.";
for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
userGroups = userGroups.substr(0, userGroups.length()-1);
+ }else{
+ //sanity check for group names
+ SharedUtil util;
+ util.setGroups(Groups, groupMap->namesOfGroups);
}
//put groups in map to find easier
if (m->control_pressed) {
if (lastlist != NULL) { delete lastlist; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete groupMap; return 0;
}
if (lastlist != NULL) { delete lastlist; }
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; }
//set fasta file as new current fastafile
string current = "";
//go through each bin, find out if shared
for (int i = 0; i < shared->getNumBins(); i++) {
- if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
+ if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
bool uniqueOTU = true;
outNames.close();
if (!wroteSomething) {
- remove(outputFileNames.c_str());
+ m->mothurRemove(outputFileNames);
string outputString = "\t" + toString(num) + " - No otus shared by groups";
string groupString = "";