added template=self capability to chimers.slayer, worked on corr.axes and added accno...

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 39c4fe001c8b9b19ef31c5a9a7f3ad98213301d6..d40dcc6a30d20080770ac806855295f98ed83df3 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -14,7 +14,7 @@
 //**********************************************************************************************************************
 vector<string> GetSeqsCommand::getValidParameters(){   
        try {
-               string Array[] =  {"fasta","name", "group", "qfile","alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"};
+               string Array[] =  {"fasta","name", "group", "qfile","alignreport", "accnos", "accnos2","dups", "list","taxonomy","outputdir","inputdir"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }
@@ -36,6 +36,7 @@ GetSeqsCommand::GetSeqsCommand(){
                outputTypes["alignreport"] = tempOutNames;
                outputTypes["list"] = tempOutNames;
                outputTypes["qfile"] = tempOutNames;
+               outputTypes["accnosreport"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
@@ -75,7 +76,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport", "qfile", "accnos", "dups", "list","taxonomy","outputdir","inputdir"};
+                       string Array[] =  {"fasta","name", "group", "alignreport", "qfile", "accnos", "accnos2","dups", "list","taxonomy","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -98,6 +99,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        outputTypes["alignreport"] = tempOutNames;
                        outputTypes["list"] = tempOutNames;
                        outputTypes["qfile"] = tempOutNames;
+                       outputTypes["accnosreport"] = tempOutNames;
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
@@ -131,6 +133,14 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                        if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
                                }
                                
+                               it = parameters.find("accnos2");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["accnos2"] = inputDir + it->second;          }
+                               }
+                               
                                it = parameters.find("list");
                                //user has given a template file
                                if(it != parameters.end()){ 
@@ -178,6 +188,9 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        if (accnosfile == "not open") { abort = true; }
                        else if (accnosfile == "not found") {  accnosfile = "";  m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }       
                        
+                       accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
+                       if (accnosfile2 == "not open") { abort = true; }
+                       
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
@@ -210,7 +223,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
                        dups = m->isTrue(temp);
                        
-                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
+                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
                
                        if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }                       
 
@@ -253,13 +266,14 @@ int GetSeqsCommand::execute(){
                if (m->control_pressed) { return 0; }
                
                //read through the correct file and output lines you want to keep
-               if (namefile != "")                     {               readName();             }
-               if (fastafile != "")            {               readFasta();    }
-               if (groupfile != "")            {               readGroup();    }
-               if (alignfile != "")            {               readAlign();    }
-               if (listfile != "")                     {               readList();             }
-               if (taxfile != "")                      {               readTax();              }
-               if (qualfile != "")                     {               readQual();             }
+               if (namefile != "")                     {               readName();                     }
+               if (fastafile != "")            {               readFasta();            }
+               if (groupfile != "")            {               readGroup();            }
+               if (alignfile != "")            {               readAlign();            }
+               if (listfile != "")                     {               readList();                     }
+               if (taxfile != "")                      {               readTax();                      }
+               if (qualfile != "")                     {               readQual();                     }
+               if (accnosfile2 != "")          {               compareAccnos();        }
                
                if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
                
@@ -746,6 +760,73 @@ int GetSeqsCommand::readAccnos(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+
+int GetSeqsCommand::compareAccnos(){
+       try {
+               
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";
+               ofstream out;
+               m->openOutputFile(outputFileName, out);
+               
+               ifstream in;
+               m->openInputFile(accnosfile2, in);
+               string name;
+               
+               set<string> namesAccnos2;
+               set<string> namesDups;
+               set<string> namesAccnos = names;
+               
+               while(!in.eof()){
+                       in >> name;
+                       
+                       if (namesAccnos.count(name) == 0){ //name unique to accnos2
+                               namesAccnos2.insert(name);
+                       }else { //you are in both so erase
+                               namesAccnos.erase(name);
+                               namesDups.insert(name);
+                       }
+                       
+                       m->gobble(in);
+               }
+               in.close();     
+               
+               out << "Names in both files : " + toString(namesDups.size()) << endl;
+               m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
+               
+               for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
+                       out << (*it) << endl;
+               }
+               
+               out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
+               m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
+               
+               for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
+                       out << (*it) << endl;
+               }
+               
+               out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
+               m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
+               
+               for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
+                       out << (*it) << endl;
+               }
+
+               out.close(); 
+               
+               outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSeqsCommand", "readAccnos");
+               exit(1);
+       }
+}
+
 
 //**********************************************************************************************************************