added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index a4697ca3fded8c34ec5320630a588e243601373d..9bf188db3d25fa4ac16b82973a2802c3b1e6ad75 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -201,21 +201,24 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                        m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); 
                                        abort = true;
                                } 
-                       }       
+                       }else { m->setAccnosFile(accnosfile); } 
                        
                        if (accnosfile2 == "not found") { accnosfile2 = ""; }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       if (fastafile == "not open") { fastafile = ""; abort = true; }
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -224,14 +227,17 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
-                       if (taxfile == "not open") { abort = true; }
+                       if (taxfile == "not open") { taxfile = ""; abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; }
                        else if (qualfile == "not found") {  qualfile = "";  }
+                       else { m->setQualFile(qualfile); }
                        
                        accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
                        if (accnosfile2 == "not open") { abort = true; }
@@ -243,6 +249,11 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        dups = m->isTrue(temp);
                        
                        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 ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+                               vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+                               parser.getNameFile(files);
+                       }
                }
 
        }
@@ -273,9 +284,8 @@ int GetSeqsCommand::execute(){
                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; }
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
                
-               m->mothurOut("Selected " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -341,10 +351,11 @@ int GetSeqsCommand::readFasta(){
                string name;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
                
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
                        
                        Sequence currSeq(in);
                        name = currSeq.getName();
@@ -355,6 +366,7 @@ int GetSeqsCommand::readFasta(){
                                        wroteSomething = true;
                                        
                                        currSeq.printSequence(out);
+                                       selectedCount++;
                                }
                        }
                        m->gobble(in);
@@ -366,6 +378,8 @@ int GetSeqsCommand::readFasta(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName); 
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
+               
                return 0;
 
        }
@@ -389,6 +403,7 @@ int GetSeqsCommand::readQual(){
                string name;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                
                while(!in.eof()){       
@@ -420,6 +435,7 @@ int GetSeqsCommand::readQual(){
                                wroteSomething = true;
                                                
                                out << name << endl << scores;
+                               selectedCount++;
                        }
                        
                        m->gobble(in);
@@ -431,6 +447,9 @@ int GetSeqsCommand::readQual(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName); 
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
+
+               
                return 0;
                
        }
@@ -452,10 +471,13 @@ int GetSeqsCommand::readList(){
                m->openInputFile(listfile, in);
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
                        
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       selectedCount = 0;
+                       
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        //read in list vector
                        ListVector list(in);
@@ -476,11 +498,11 @@ int GetSeqsCommand::readList(){
                                        binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
                                        
                                        //if that name is in the .accnos file, add it
-                                       if (names.count(name) != 0) {  newNames += name + ",";  }
+                                       if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; }
                                }
                        
                                //get last name
-                               if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
+                               if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++; }
 
                                //if there are names in this bin add to new list
                                if (newNames != "") { 
@@ -503,6 +525,8 @@ int GetSeqsCommand::readList(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
+               
                return 0;
 
        }
@@ -526,11 +550,11 @@ int GetSeqsCommand::readName(){
                string name, firstCol, secondCol;
                
                bool wroteSomething = false;
-               
+               int selectedCount = 0;
                
                while(!in.eof()){
                
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        in >> firstCol;                         
                        in >> secondCol;
@@ -552,7 +576,10 @@ int GetSeqsCommand::readName(){
                                for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
                                out << firstCol << '\t' << hold << endl;
                                wroteSomething = true;
+                               selectedCount += parsedNames.size();
                        }else {
+                               selectedCount += validSecond.size();
+                               
                                //if the name in the first column is in the set then print it and any other names in second column also in set
                                if (names.count(firstCol) != 0) {
                                
@@ -588,6 +615,8 @@ int GetSeqsCommand::readName(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
+               
                return 0;
                
        }
@@ -612,10 +641,11 @@ int GetSeqsCommand::readGroup(){
                string name, group;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
 
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 
                        in >> name;                             //read from first column
@@ -626,6 +656,7 @@ int GetSeqsCommand::readGroup(){
                                wroteSomething = true;
                                
                                out << name << '\t' << group << endl;
+                               selectedCount++;
                        }
                                        
                        m->gobble(in);
@@ -636,6 +667,9 @@ int GetSeqsCommand::readGroup(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
+
+               
                return 0;
 
        }
@@ -658,10 +692,11 @@ int GetSeqsCommand::readTax(){
                string name, tax;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
 
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        in >> name;                             //read from first column
                        in >> tax;                      //read from second column
@@ -671,6 +706,7 @@ int GetSeqsCommand::readTax(){
                                wroteSomething = true;
                                
                                out << name << '\t' << tax << endl;
+                               selectedCount++;
                        }
                                        
                        m->gobble(in);
@@ -680,6 +716,8 @@ int GetSeqsCommand::readTax(){
                
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
+               
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
                        
                return 0;
 
@@ -705,6 +743,7 @@ int GetSeqsCommand::readAlign(){
                string name, junk;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                //read column headers
                for (int i = 0; i < 16; i++) {  
@@ -715,7 +754,7 @@ int GetSeqsCommand::readAlign(){
                
                while(!in.eof()){
                
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 
                        in >> name;                             //read from first column
@@ -723,6 +762,7 @@ int GetSeqsCommand::readAlign(){
                        //if this name is in the accnos file
                        if (names.count(name) != 0) {
                                wroteSomething = true;
+                               selectedCount++;
                                
                                out << name << '\t';
                                
@@ -749,6 +789,8 @@ int GetSeqsCommand::readAlign(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
+               
                return 0;
                
        }