paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index df97fd88ad471ba97daaa593233d4177f1fe21a2..6f7657f3da640514fb5125527b17cfd779a5cad0 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "deconvolutecommand.h"
+#include "sequence.hpp"
 
 //**********************************************************************************************************************
 vector<string> DeconvoluteCommand::setParameters(){    
@@ -144,15 +145,95 @@ int DeconvoluteCommand::execute() {
                string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
                string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
                
-               FastaMap fastamap;
-       
-               if(oldNameMapFName == "")       {       fastamap.readFastaFile(inFastaName);                                    }
-               else                                            {       fastamap.readFastaFile(inFastaName, oldNameMapFName);   }
+               map<string, string> nameMap;
+               map<string, string>::iterator itNames;
+               if (oldNameMapFName != "")  {  m->readNames(oldNameMapFName, nameMap); }
                
                if (m->control_pressed) { return 0; }
                
-               fastamap.printCondensedFasta(outFastaFile);
-               fastamap.printNamesFile(outNameFile);
+               ifstream in; 
+               m->openInputFile(inFastaName, in);
+               
+               ofstream outFasta;
+               m->openOutputFile(outFastaFile, outFasta);
+               
+               map<string, string> sequenceStrings; //sequenceString -> list of names.  "atgc...." -> seq1,seq2,seq3.
+               map<string, string>::iterator itStrings;
+               set<string> nameInFastaFile; //for sanity checking
+               set<string>::iterator itname;
+               int count = 0;
+               while (!in.eof()) {
+                       
+                       if (m->control_pressed) { in.close(); outFasta.close(); remove(outFastaFile.c_str()); return 0; }
+                       
+                       Sequence seq(in);
+                       
+                       if (seq.getName() != "") {
+                               
+                               //sanity checks
+                               itname = nameInFastaFile.find(seq.getName());
+                               if (itname == nameInFastaFile.end()) { nameInFastaFile.insert(seq.getName());  }
+                               else { m->mothurOut("[ERROR]: You already have a sequence named " + seq.getName() + " in your fasta file, sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
+                               itStrings = sequenceStrings.find(seq.getAligned());
+                               
+                               if (itStrings == sequenceStrings.end()) { //this is a new unique sequence
+                                       //output to unique fasta file
+                                       seq.printSequence(outFasta);
+                                       
+                                       if (oldNameMapFName != "") {
+                                               itNames = nameMap.find(seq.getName());
+                                               
+                                               if (itNames == nameMap.end()) { //namefile and fastafile do not match
+                                                       m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
+                                               }else {
+                                                       sequenceStrings[seq.getAligned()] = itNames->second;
+                                               }
+                                       }else { sequenceStrings[seq.getAligned()] = seq.getName();      }
+                               }else { //this is a dup
+                                       if (oldNameMapFName != "") {
+                                               itNames = nameMap.find(seq.getName());
+                                               
+                                               if (itNames == nameMap.end()) { //namefile and fastafile do not match
+                                                       m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
+                                               }else {
+                                                       sequenceStrings[seq.getAligned()] += "," + itNames->second;
+                                               }
+                                       }else { sequenceStrings[seq.getAligned()] += "," + seq.getName();       }
+                               }
+                               
+                               count++;
+                       }
+                       
+                       m->gobble(in);
+                       
+                       if(count % 1000 == 0)   { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine();       }
+               }
+               
+               if(count % 1000 != 0)   { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine();       }
+               
+               in.close();
+               outFasta.close();
+               
+               if (m->control_pressed) { remove(outFastaFile.c_str()); return 0; }
+               
+               //print new names file
+               ofstream outNames;
+               m->openOutputFile(outNameFile, outNames);
+               
+               for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
+                       if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); outNames.close(); remove(outNameFile.c_str()); return 0; }
+                       
+                       //get rep name
+                       int pos = (itStrings->second).find_first_of(',');
+                       
+                       if (pos == string::npos) { // only reps itself
+                               outNames << itStrings->second << '\t' << itStrings->second << endl;
+                       }else {
+                               outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
+                       }
+               }
+               outNames.close();
                
                if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }