added taxonomy file to list of files list.seqs, get.seqs and remove.seqs can process

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 7fdf6ed7084463b4e875c8fa01a4e4f9b13db513..a9463a076cfee738f5171575325a6a92881744d9 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -22,7 +22,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","outputdir","inputdir"};
+                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","taxonomy","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -91,6 +91,14 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
+                               
+                               it = parameters.find("taxonomy");
+                               //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["taxonomy"] = inputDir + it->second;         }
+                               }
                        }
 
                        
@@ -119,13 +127,12 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
                        
-                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or listfile."); m->mothurOutEndLine(); abort = true; }
-                       
-                       int okay = 2;
-                       if (outputDir != "") { okay++; }
-                       if (inputDir != "")     { okay++; }
+                       taxfile = validParameter.validFile(parameters, "taxonomy", true);
+                       if (taxfile == "not open") { abort = true; }
+                       else if (taxfile == "not found") {  taxfile = "";  }
+
                        
-                       if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); m->mothurOutEndLine(); abort = true;  }
+                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
                }
 
        }
@@ -138,9 +145,9 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
 
 void GetSeqsCommand::help(){
        try {
-               m->mothurOut("The get.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
+               m->mothurOut("The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy or alignreport file.\n");
                m->mothurOut("It outputs a file containing only the sequences in the .accnos file.\n");
-               m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list and alignreport.  You must provide accnos and one of the other parameters.\n");
+               m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy and alignreport.  You must provide accnos and at least one of the other parameters.\n");
                m->mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
                m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
@@ -165,12 +172,13 @@ int GetSeqsCommand::execute(){
                
                //read through the correct file and output lines you want to keep
                if (fastafile != "")            {               readFasta();    }
-               else if (namefile != "")        {               readName();             }
-               else if (groupfile != "")       {               readGroup();    }
-               else if (alignfile != "")       {               readAlign();    }
-               else if (listfile != "")        {               readList();             }
+               if (namefile != "")                     {               readName();             }
+               if (groupfile != "")            {               readGroup();    }
+               if (alignfile != "")            {               readAlign();    }
+               if (listfile != "")                     {               readList();             }
+               if (taxfile != "")                      {               readTax();              }
                
-               if (m->control_pressed) { return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -216,8 +224,6 @@ int GetSeqsCommand::readFasta(){
                                        wroteSomething = true;
                                        
                                        currSeq.printSequence(out);
-                                       
-                                       names.erase(name);
                                }
                        }
                        gobble(in);
@@ -427,8 +433,6 @@ int GetSeqsCommand::readGroup(){
                                wroteSomething = true;
                                
                                out << name << '\t' << group << endl;
-                               
-                               names.erase(name);
                        }
                                        
                        gobble(in);
@@ -449,7 +453,52 @@ int GetSeqsCommand::readGroup(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+int GetSeqsCommand::readTax(){
+       try {
+               if (outputDir == "") { outputDir += hasPath(taxfile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(taxfile)) + "pick" + getExtension(taxfile);
+               ofstream out;
+               openOutputFile(outputFileName, out);
+               
+               ifstream in;
+               openInputFile(taxfile, in);
+               string name, tax;
+               
+               bool wroteSomething = false;
+               
+               while(!in.eof()){
+
+                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 
+                       in >> name;                             //read from first column
+                       in >> tax;                      //read from second column
+                       
+                       //if this name is in the accnos file
+                       if (names.count(name) == 1) {
+                               wroteSomething = true;
+                               
+                               out << name << '\t' << tax << endl;
+                       }
+                                       
+                       gobble(in);
+               }
+               in.close();
+               out.close();
+               
+               if (wroteSomething == false) {
+                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
+                       remove(outputFileName.c_str()); 
+               }else {  outputNames.push_back(outputFileName); }
+               
+               return 0;
+
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSeqsCommand", "readTax");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 int GetSeqsCommand::readAlign(){
@@ -493,8 +542,6 @@ int GetSeqsCommand::readAlign(){
                                }
                                out << endl;
                                
-                               names.erase(name);
-                               
                        }else {//still read just don't do anything with it
                                //read rest
                                for (int i = 0; i < 15; i++) {  

diff --git a/getseqscommand.h b/getseqscommand.h
index b574afe38734a789fa39985090012cff358d2e95..9d8e7960f5c2e949f021602aaf1aa36e7d3e82e0 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -24,7 +24,7 @@ class GetSeqsCommand : public Command {
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
+               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
                bool abort;
                
                int readFasta();
@@ -33,6 +33,7 @@ class GetSeqsCommand : public Command {
                int readAlign();
                int readAccnos();
                int readList();
+               int readTax();
                
 };
 

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 23c71ecdcf2ac06f522f034cbea813d4a1f2cd22..3200137343e8691e2e8df3f70fcd1940f933b88c 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -22,7 +22,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport","list","outputdir","inputdir"};
+                       string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -83,6 +83,14 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
+                               
+                               it = parameters.find("taxonomy");
+                               //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["taxonomy"] = inputDir + it->second;         }
+                               }
                        }
 
                        //check for required parameters
@@ -106,8 +114,11 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
 
+                       taxfile = validParameter.validFile(parameters, "taxonomy", true);
+                       if (taxfile == "not open") { abort = true; }
+                       else if (taxfile == "not found") {  taxfile = "";  }
                        
-                       if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
+                       if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
                        
                        int okay = 1;
                        if (outputDir != "") { okay++; }
@@ -126,8 +137,8 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 
 void ListSeqsCommand::help(){
        try {
-               m->mothurOut("The list.seqs command reads a fasta, name, group, list or alignreport file and outputs a .accnos file containing sequence names.\n");
-               m->mothurOut("The list.seqs command parameters are fasta, name, group and alignreport.  You must provide one of these parameters.\n");
+               m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n");
+               m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n");
                m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
                m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
@@ -151,6 +162,7 @@ int ListSeqsCommand::execute(){
                else if (groupfile != "")       {       inputFileName = groupfile;      readGroup();    }
                else if (alignfile != "")       {       inputFileName = alignfile;      readAlign();    }
                else if (listfile != "")        {       inputFileName = listfile;       readList();             }
+               else if (taxfile != "")         {       inputFileName = taxfile;        readTax();              }
                
                if (m->control_pressed) { return 0; }
                
@@ -364,3 +376,32 @@ int ListSeqsCommand::readAlign(){
        }
 }
 //**********************************************************************************************************************
+int ListSeqsCommand::readTax(){
+       try {
+               
+               ifstream in;
+               openInputFile(taxfile, in);
+               string name, firstCol, secondCol;
+               
+               while(!in.eof()){
+               
+                       if (m->control_pressed) { in.close(); return 0; }
+
+                       in >> firstCol;                         
+                       in >> secondCol;                        
+                       
+                       names.push_back(firstCol);
+                       
+                       gobble(in);
+               }
+               in.close();
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ListSeqsCommand", "readTax");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************

diff --git a/listseqscommand.h b/listseqscommand.h
index 391ec9a46b9f09671f79fbc0f895730338570d4c..6a210a180e5bc9453005c7aefb8613fa45d52c03 100644 (file)
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -23,7 +23,7 @@ class ListSeqsCommand : public Command {
                
        private:
                vector<string> names;
-               string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile;
+               string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
                bool abort;
                
                int readFasta();
@@ -31,6 +31,7 @@ class ListSeqsCommand : public Command {
                int readGroup();
                int readAlign();
                int readList();
+               int readTax();
                
 };
 

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index a61e467e0bd5820060c052acffefe5fe7983294f..da6bc44297d474e75d9866c69ff3d790ae92052a 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -22,7 +22,7 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","outputdir","inputdir", "dups" };
+                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","taxonomy","outputdir","inputdir", "dups" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -91,6 +91,14 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
+                               
+                               it = parameters.find("taxonomy");
+                               //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["taxonomy"] = inputDir + it->second;         }
+                               }
                        }
 
                        
@@ -119,19 +127,18 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
                        
+                       taxfile = validParameter.validFile(parameters, "taxonomy", true);
+                       if (taxfile == "not open") { abort = true; }
+                       else if (taxfile == "not found") {  taxfile = "";  }
+
+                       
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
                        dups = isTrue(temp);
                        
-                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); m->mothurOutEndLine(); abort = true; }
-                       
-                       //int okay = 2;
-                       //if (outputDir != "") { okay++; }
-                       //if (usedDups != "") { okay++;  }
+                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, alignreport or list."); m->mothurOutEndLine(); abort = true; }
                        
-                       if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
-                       
-                       //if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true;  }
+                       if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }                       
                }
 
        }
@@ -144,9 +151,9 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
 
 void RemoveSeqsCommand::help(){
        try {
-               m->mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
+               m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy or alignreport file.\n");
                m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
-               m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, alignreport and dups.  You must provide accnos and one of the file parameters.\n");
+               m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, alignreport and dups.  You must provide accnos and at least one of the file parameters.\n");
                m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. If dups=true, then remove.seqs outputs a new .accnos file containing all the sequences removed. \n");
                m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
                m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
@@ -176,6 +183,7 @@ int RemoveSeqsCommand::execute(){
                if (groupfile != "")            {               readGroup();    }
                if (alignfile != "")            {               readAlign();    }
                if (listfile != "")                     {               readList();             }
+               if (taxfile != "")                      {               readTax();              }
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
                
@@ -221,7 +229,7 @@ int RemoveSeqsCommand::readFasta(){
                                        wroteSomething = true;
                                        
                                        currSeq.printSequence(out);
-                               }//else {               names.erase(name);              }
+                               }
                        }
                        gobble(in);
                }
@@ -435,7 +443,7 @@ int RemoveSeqsCommand::readGroup(){
                        if (names.count(name) == 0) {
                                wroteSomething = true;
                                out << name << '\t' << group << endl;
-                       }//else {               names.erase(name);              }
+                       }
                                        
                        gobble(in);
                }
@@ -454,7 +462,49 @@ int RemoveSeqsCommand::readGroup(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+int RemoveSeqsCommand::readTax(){
+       try {
+               if (outputDir == "") {  outputDir += hasPath(taxfile);  }
+               string outputFileName = outputDir + getRootName(getSimpleName(taxfile)) + "pick" + getExtension(taxfile);
+               ofstream out;
+               openOutputFile(outputFileName, out);
 
+               ifstream in;
+               openInputFile(taxfile, in);
+               string name, tax;
+               
+               bool wroteSomething = false;
+               
+               while(!in.eof()){
+                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       
+                       in >> name;                             //read from first column
+                       in >> tax;                      //read from second column
+                       
+                       //if this name is in the accnos file
+                       if (names.count(name) == 0) {
+                               wroteSomething = true;
+                               out << name << '\t' << tax << endl;
+                       }
+                                       
+                       gobble(in);
+               }
+               in.close();
+               out.close();
+               
+               if (wroteSomething == false) {
+                       m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
+                       remove(outputFileName.c_str()); 
+               }else { outputNames.push_back(outputFileName); }
+               
+               return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RemoveSeqsCommand", "readTax");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 int RemoveSeqsCommand::readAlign(){
@@ -496,7 +546,6 @@ int RemoveSeqsCommand::readAlign(){
                                out << endl;
                                
                        }else {//still read just don't do anything with it
-                               //names.erase(name);    
                                
                                //read rest
                                for (int i = 0; i < 15; i++) {  

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 1f429d92810402f64a1c2d776510719aa7113610..8238c649489e3dff52371fa06ab8e2f49b93258f 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -23,7 +23,7 @@ class RemoveSeqsCommand : public Command {
                
        private:
                set<string> names;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
+               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
                bool abort, dups;
                vector<string> outputNames;
                
@@ -33,6 +33,7 @@ class RemoveSeqsCommand : public Command {
                int readAlign();
                void readAccnos();
                int readList();
+               int readTax();
                
 };