added keep dots to pcr.seqs. fixed pre.cluster name file name when group option is...

[mothur.git] / prcseqscommand.cpp

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 7f34a03d353da5a6aa2facec462693521fdda3f4..afedc746360b495850d588b6c7ce3839ec3f9256 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -23,6 +23,7 @@ vector<string> PcrSeqsCommand::setParameters(){
                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);
         CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
         
@@ -177,6 +178,9 @@ PcrSeqsCommand::PcrSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "keepprimer", false);  if (temp == "not found")    {        temp = "f";     }
                        keepprimer = m->isTrue(temp);   
             
+            temp = validParameter.validFile(parameters, "keepdots", false);  if (temp == "not found")    {     temp = "t";     }
+                       keepdots = m->isTrue(temp);     
+            
                        temp = validParameter.validFile(parameters, "oligos", true);
                        if (temp == "not found"){       oligosfile = "";                }
                        else if(temp == "not open"){    oligosfile = ""; abort = true;  } 
@@ -223,7 +227,7 @@ PcrSeqsCommand::PcrSeqsCommand(string option)  {
                 m->mothurOut("[ERROR]: You did not set any options. Please provide an oligos or ecoli file, or set start or end.\n"); abort = true;
             }
             
-            if ((oligosfile == "") && (ecolifile == "") && (start < 0) && (end != -1)) { m->mothurOut("[ERROR]: Invalid start value.\n"); abort = true; }
+            if ((oligosfile == "") && (ecolifile == "") && (start < 0) && (end == -1)) { m->mothurOut("[ERROR]: Invalid start value.\n"); abort = true; }
             
             if ((ecolifile != "") && (start != -1) && (end != -1)) {
                 m->mothurOut("[ERROR]: You provided an ecoli file , but set the start or end parameters. Unsure what you intend.  When you provide the ecoli file, mothur thinks you want to use the start and end of the sequence in the ecoli file.\n"); abort = true;
@@ -297,7 +301,10 @@ int PcrSeqsCommand::execute(){
                
                if (m->control_pressed) {  return 0; }          
         
-        writeAccnos(badNames);      
+        //don't write or keep if blank
+        if (badNames.size() != 0)   { writeAccnos(badNames);        }   
+        if (m->isBlank(badSeqFile)) { m->mothurRemove(badSeqFile);  }
+        
         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
         if (namefile != "")                    {               readName(badNames);             }   
         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
@@ -434,7 +441,7 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
             if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
             
                        // Allocate memory for thread data.
-                       pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, m, oligosfile, ecolifile, primers, revPrimer, nomatch, keepprimer, start, end, length, lines[i].start, lines[i].end);
+                       pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, m, oligosfile, ecolifile, primers, revPrimer, nomatch, keepprimer, keepdots, start, end, length, lines[i].start, lines[i].end);
                        pDataArray.push_back(tempPcr);
                        
                        //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
@@ -516,8 +523,14 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
                         else{
                             //are you aligned
                             if (aligned) { 
-                                if (!keepprimer)    {  currSeq.padToPos(mapAligned[primerEnd]); } 
-                                else                {  currSeq.padToPos(mapAligned[primerStart]); }
+                                if (!keepprimer)    {  
+                                    if (keepdots)   { currSeq.filterToPos(mapAligned[primerEnd]);   }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerEnd]));                                              }
+                                } 
+                                else                {  
+                                    if (keepdots)   { currSeq.filterToPos(mapAligned[primerStart]);  }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart]));                                              }
+                                }
                             }else { 
                                 if (!keepprimer)    { currSeq.setAligned(currSeq.getUnaligned().substr(primerEnd)); } 
                                 else                { currSeq.setAligned(currSeq.getUnaligned().substr(primerStart)); } 
@@ -533,8 +546,14 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
                         else{ 
                             //are you aligned
                             if (aligned) { 
-                                if (!keepprimer)    {  currSeq.padFromPos(mapAligned[primerStart]); } 
-                                else                {  currSeq.padFromPos(mapAligned[primerEnd]); } 
+                                if (!keepprimer)    {  
+                                    if (keepdots)   { currSeq.filterFromPos(mapAligned[primerStart]); }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerStart]));   }
+                                } 
+                                else                {  
+                                    if (keepdots)   { currSeq.filterFromPos(mapAligned[primerEnd]); }
+                                    else            { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerEnd]));   }
+                                } 
                             }
                             else { 
                                 if (!keepprimer)    { currSeq.setAligned(currSeq.getUnaligned().substr(0, primerStart));   } 
@@ -549,19 +568,35 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
                     else if (currSeq.getAligned().length() != length) {
                         m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); m->control_pressed = true; break; 
                     }else {
-                        currSeq.padToPos(start); 
-                        currSeq.padFromPos(end);
+                        if (keepdots)   { 
+                            currSeq.filterToPos(start); 
+                            currSeq.filterFromPos(end);
+                        }else {
+                            string seqString = currSeq.getAligned().substr(0, end);
+                            seqString = seqString.substr(start);
+                            currSeq.setAligned(seqString); 
+                        }
                     }
                 }else{ //using start and end to trim
                     //make sure the seqs are aligned
                     lengths.insert(currSeq.getAligned().length());
                     if (lengths.size() > 1) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
                     else {
-                        if (start != -1) { currSeq.padToPos(start); }
                         if (end != -1) {
                             if (end > currSeq.getAligned().length()) {  m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); m->control_pressed = true; break; }
                             else {
-                                currSeq.padFromPos(end);
+                                if (keepdots)   { currSeq.filterFromPos(end); }
+                                else {
+                                    string seqString = currSeq.getAligned().substr(0, end);
+                                    currSeq.setAligned(seqString); 
+                                }
+                            }
+                        }
+                        if (start != -1) { 
+                            if (keepdots)   {  currSeq.filterToPos(start);  }
+                            else {
+                                string seqString = currSeq.getAligned().substr(start);
+                                currSeq.setAligned(seqString); 
                             }
                         }
                     }