forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / prcseqscommand.cpp

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index afedc746360b495850d588b6c7ce3839ec3f9256..725136bf56a2512355cf170634b625bfa5df1581 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -20,7 +20,6 @@ vector<string> PcrSeqsCommand::setParameters(){
                CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
                CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
                CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "",false,false); parameters.push_back(pnomatch);
-               CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
         CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
@@ -40,8 +39,15 @@ vector<string> PcrSeqsCommand::setParameters(){
 string PcrSeqsCommand::getHelpString(){        
        try {
                string helpString = "";
-               helpString += "The pcr.seqs command reads a fasta file ...\n";
-               
+               helpString += "The pcr.seqs command reads a fasta file.\n";
+        helpString += "The pcr.seqs command parameters are fasta, oligos, name, group, taxonomy, ecoli, start, end, nomatch, processors, keepprimer and keepdots.\n";
+               helpString += "The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence.\n";
+        helpString += "The start parameter allows you to provide a starting position to trim to.\n";
+        helpString += "The end parameter allows you to provide a ending position to trim from.\n";
+        helpString += "The nomatch parameter allows you to decide what to do with sequences where the primer is not found. Default=reject, meaning remove from fasta file.  if nomatch=true, then do nothing to sequence.\n";
+        helpString += "The processors parameter allows you to use multiple processors.\n";
+        helpString += "The keepprimer parameter allows you to keep the primer, default=false.\n";
+        helpString += "The keepdots parameter allows you to keep the leading and trailing .'s, default=true.\n";
                helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
                helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Pcr.seqs .\n";
                return helpString;
@@ -159,8 +165,6 @@ PcrSeqsCommand::PcrSeqsCommand(string option)  {
                                
                        }
             
-            //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 = ""; }
                        
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
@@ -171,7 +175,9 @@ PcrSeqsCommand::PcrSeqsCommand(string option)  {
                        }else if (fastafile == "not open") { fastafile = ""; abort = true; }    
                        else { m->setFastaFile(fastafile); }
                        
-            
+            //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 = m->hasPath(fastafile);      }
+
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        string temp;
@@ -204,10 +210,7 @@ PcrSeqsCommand::PcrSeqsCommand(string option)  {
                        if (taxfile == "not found"){    taxfile = "";           }
                        else if(taxfile == "not open"){ taxfile = ""; abort = true;     } 
             else { m->setTaxonomyFile(taxfile); }
-                       
-                       temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
-                       m->mothurConvert(temp, pdiffs);
-                       
+                                               
                        temp = validParameter.validFile(parameters, "start", false);    if (temp == "not found") { temp = "-1"; }
                        m->mothurConvert(temp, start);
             
@@ -266,7 +269,7 @@ int PcrSeqsCommand::execute(){
                outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
         
         string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pcr.scrap.fasta";
-               outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile);
+               
                
         length = 0;
                if(oligosfile != ""){    readOligos();     }  if (m->control_pressed) {  return 0; }
@@ -304,6 +307,7 @@ int PcrSeqsCommand::execute(){
         //don't write or keep if blank
         if (badNames.size() != 0)   { writeAccnos(badNames);        }   
         if (m->isBlank(badSeqFile)) { m->mothurRemove(badSeqFile);  }
+        else { outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile); }
         
         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
         if (namefile != "")                    {               readName(badNames);             }   
@@ -601,7 +605,10 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
                         }
                     }
                 }
-                                    
+                
+                //trimming removed all bases
+                if (currSeq.getUnaligned() == "") { goodSeq = false; }
+                
                                if(goodSeq == 1)    {   currSeq.printSequence(goodFile);        }
                                else {  
                     badSeqNames.insert(currSeq.getName());