added current as option is lists of file names, processors now outputted with current...

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 0b7f3f09abbd26026de0cb2602d08d0a0e4fa514..7318f9060cdbf5fa2aa5d23205163c1dfecc048a 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -16,6 +16,7 @@ vector<string> ScreenSeqsCommand::setParameters(){
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
                CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
                CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
                CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
                CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
@@ -43,7 +44,7 @@ string ScreenSeqsCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The screen.seqs command reads a fastafile and creates .....\n";
-               helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, optimize, criteria and processors.\n";
+               helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, optimize, criteria and processors.\n";
                helpString += "The fasta parameter is required.\n";
                helpString += "The start parameter .... The default is -1.\n";
                helpString += "The end parameter .... The default is -1.\n";
@@ -78,6 +79,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(){
                outputTypes["group"] = tempOutNames;
                outputTypes["alignreport"] = tempOutNames;
                outputTypes["accnos"] = tempOutNames;
+               outputTypes["qfile"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
@@ -114,6 +116,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                        outputTypes["group"] = tempOutNames;
                        outputTypes["alignreport"] = tempOutNames;
                        outputTypes["accnos"] = tempOutNames;
+                       outputTypes["qfile"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -151,6 +154,15 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
                                }
+                               
+                               it = parameters.find("qfile");
+                               //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["qfile"] = inputDir + it->second;            }
+                               }
+                               
                        }
 
                        //check for required parameters
@@ -166,6 +178,10 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
                        
+                       qualfile = validParameter.validFile(parameters, "qfile", true);
+                       if (qualfile == "not open") { abort = true; }   
+                       else if (qualfile == "not found") { qualfile = ""; }
+                       
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
@@ -461,6 +477,7 @@ int ScreenSeqsCommand::execute(){
                if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
 
                if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
+               if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
                
                if (m->control_pressed) { remove(goodSeqFile.c_str());  return 0; }
                
@@ -492,6 +509,11 @@ int ScreenSeqsCommand::execute(){
                if (itTypes != outputTypes.end()) {
                        if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
                }
+               
+               itTypes = outputTypes.find("qfile");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+               }
 
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
                m->mothurOutEndLine();
@@ -906,6 +928,79 @@ int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
                exit(1);
        }
        
+}
+//***************************************************************************************************************
+
+int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
+       try {
+               ifstream in;
+               m->openInputFile(qualfile, in);
+               set<string>::iterator it;
+               
+               string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
+               outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
+               ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
+               
+               while(!in.eof()){       
+                       
+                       if (m->control_pressed) { goodQual.close(); in.close(); remove(goodQualFile.c_str()); return 0; }
+
+                       string saveName = "";
+                       string name = "";
+                       string scores = "";
+                       
+                       in >> name; 
+                       
+                       if (name.length() != 0) { 
+                               saveName = name.substr(1);
+                               while (!in.eof())       {       
+                                       char c = in.get(); 
+                                       if (c == 10 || c == 13){        break;  }
+                                       else { name += c; }     
+                               } 
+                               m->gobble(in);
+                       }
+                       
+                       while(in){
+                               char letter= in.get();
+                               if(letter == '>'){      in.putback(letter);     break;  }
+                               else{ scores += letter; }
+                       }
+                       
+                       m->gobble(in);
+                       
+                       it = badSeqNames.find(saveName);
+                       
+                       if(it != badSeqNames.end()){
+                               badSeqNames.erase(it);
+                       }else{                          
+                               goodQual << name << endl << scores;
+                       }
+                       
+                       m->gobble(in);
+               }
+               
+               in.close();
+               goodQual.close();
+               
+               //we were unable to remove some of the bad sequences
+               if (badSeqNames.size() != 0) {
+                       for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {  
+                               m->mothurOut("Your qual file does not include the sequence " + *it + " please correct."); 
+                               m->mothurOutEndLine();
+                       }
+               }
+               
+               if (m->control_pressed) {  remove(goodQualFile.c_str());  return 0; }
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ScreenSeqsCommand", "screenQual");
+               exit(1);
+       }
+       
 }
 //**********************************************************************************************************************