working on pam

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index d10dfb4935c390d0353976eeb5c182340519ebfb..0ead54a90cf2ef44205947baddecb39b21e6b8f7 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -16,6 +16,7 @@
 //**********************************************************************************************************************
 vector<string> ListSeqsCommand::setParameters(){       
        try {
+        CommandParameter pfastq("fastq", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfastq);
                CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfasta);
                CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pname);
         CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pcount);
@@ -39,8 +40,8 @@ vector<string> ListSeqsCommand::setParameters(){
 string ListSeqsCommand::getHelpString(){       
        try {
                string helpString = "";
-               helpString += "The list.seqs command reads a fasta, name, group, count, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
-               helpString += "The list.seqs command parameters are fasta, name, group, count, list, taxonomy and alignreport.  You must provide one of these parameters.\n";
+               helpString += "The list.seqs command reads a fasta, name, group, count, list, taxonomy, fastq or alignreport file and outputs a .accnos file containing sequence names.\n";
+               helpString += "The list.seqs command parameters are fasta, name, group, count, list, taxonomy, fastq and alignreport.  You must provide one of these parameters.\n";
                helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
                helpString += "Example list.seqs(fasta=amazon.fasta).\n";
                helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
@@ -169,6 +170,14 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["count"] = inputDir + it->second;            }
                                }
+                
+                it = parameters.find("fastq");
+                               //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["fastq"] = inputDir + it->second;            }
+                               }
                        }
 
                        //check for required parameters
@@ -205,8 +214,12 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        if (countfile == "not open") { abort = true; }
                        else if (countfile == "not found") {  countfile = "";  }
                        else { m->setCountTableFile(countfile); }
+            
+            fastqfile = validParameter.validFile(parameters, "fastq", true);
+                       if (fastqfile == "not open") { abort = true; }
+                       else if (fastqfile == "not found") {  fastqfile = "";  }
                        
-                       if ((countfile == "") && (fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
+                       if ((fastqfile == "") && (countfile == "") && (fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
                        
                        int okay = 1;
                        if (outputDir != "") { okay++; }
@@ -230,6 +243,7 @@ int ListSeqsCommand::execute(){
                
                //read functions fill names vector
                if (fastafile != "")            {       inputFileName = fastafile;      readFasta();    }
+        else if (fastqfile != "")      {       inputFileName = fastqfile;      readFastq();    }
                else if (namefile != "")        {       inputFileName = namefile;       readName();             }
                else if (groupfile != "")       {       inputFileName = groupfile;      readGroup();    }
                else if (alignfile != "")       {       inputFileName = alignfile;      readAlign();    }
@@ -285,6 +299,53 @@ int ListSeqsCommand::execute(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+int ListSeqsCommand::readFastq(){
+       try {
+               
+               ifstream in;
+               m->openInputFile(fastqfile, in);
+               string name;
+               
+               //ofstream out;
+               //string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+               //m->openOutputFile(newFastaName, out);
+               int count = 1;
+               //string lastName = "";
+               
+               while(!in.eof()){
+                       
+                       if (m->control_pressed) { in.close(); return 0; }
+                       
+                       //read sequence name
+                       string name = m->getline(in); m->gobble(in);
+                       
+                       if (name[0] == '@') {
+                vector<string> splits = m->splitWhiteSpace(name);
+                name = splits[0];
+                name = name.substr(1);
+                m->checkName(name);
+                names.push_back(name);
+                //get rest of lines
+                name = m->getline(in); m->gobble(in);
+                name = m->getline(in); m->gobble(in);
+                name = m->getline(in); m->gobble(in);
+            }
+                       
+                       m->gobble(in);
+                       if (m->debug) { count++; cout << "[DEBUG]: count = " + toString(count) + ", name = " + name + "\n"; }
+               }
+               in.close();
+               //out.close();
+               
+               return 0;
+        
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ListSeqsCommand", "readFastq");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 int ListSeqsCommand::readFasta(){
@@ -415,7 +476,7 @@ int ListSeqsCommand::readGroup(){
 int ListSeqsCommand::readCount(){
        try {
                CountTable ct;
-               ct.readTable(countfile);
+               ct.readTable(countfile, false, false);
         
         if (m->control_pressed) { return 0; }