adds group parameter to chimera.uchime so you can check for chimeras with template...

[mothur.git] / sequenceparser.cpp

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index 44012d8ba8321fea520fbe613e0dac8f8911c760..e60f19b0df0034de0c1a693d7c5a55c59ef0ef82 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -106,6 +106,8 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                                                }
                                        }
                                }
+                               
+                               allSeqsMap[names[i]] = names[0];
                        }
                        
                        
@@ -247,6 +249,78 @@ vector<Sequence> SequenceParser::getSeqs(string g){
                exit(1);
        }
 }
+/************************************************************/
+int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){ 
+       try {
+               map<string, vector<Sequence> >::iterator it;
+               vector<Sequence> seqForThisGroup;
+               vector<seqPriorityNode> nameVector;
+               
+               it = seqs.find(g);
+               if(it == seqs.end()) {
+                       m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
+               }else {
+                       
+                       ofstream out;
+                       m->openOutputFile(filename, out);
+                       
+                       seqForThisGroup = it->second;
+                       
+                       if (uchimeFormat) {
+                               // format should look like 
+                               //>seqName /ab=numRedundantSeqs/
+                               //sequence
+                               
+                               map<string, string> nameMapForThisGroup = getNameMap(g);
+                               map<string, string>::iterator itNameMap;
+                               int error = 0;
+                               
+                               for (int i = 0; i < seqForThisGroup.size(); i++) {
+                                       itNameMap = nameMapForThisGroup.find(seqForThisGroup[i].getName());
+                                       
+                                       if (itNameMap == nameMapForThisGroup.end()){
+                                               error = 1;
+                                               m->mothurOut("[ERROR]: " + seqForThisGroup[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
+                                       }else {
+                                               int num = m->getNumNames(itNameMap->second);
+                                               
+                                               seqPriorityNode temp(num, seqForThisGroup[i].getAligned(), seqForThisGroup[i].getName());
+                                               nameVector.push_back(temp);
+                                       }
+                               }
+                               
+                               if (error == 1) { out.close(); m->mothurRemove(filename); return 1; }
+                               
+                               //sort by num represented
+                               sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
+
+                               //print new file in order of
+                               for (int i = 0; i < nameVector.size(); i++) {
+                                       
+                                       if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
+                                       
+                                       out << ">" << nameVector[i].name  << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl;
+                               }
+                               
+                       }else { 
+                               for (int i = 0; i < seqForThisGroup.size(); i++) {
+                                       
+                                       if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
+                                       
+                                       seqForThisGroup[i].printSequence(out);  
+                               }
+                       }
+                       out.close();
+               }
+               
+               return 0; 
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceParser", "getSeqs");
+               exit(1);
+       }
+}
+
 /************************************************************/
 map<string, string> SequenceParser::getNameMap(string g){ 
        try {
@@ -268,6 +342,38 @@ map<string, string> SequenceParser::getNameMap(string g){
        }
 }
 /************************************************************/
+int SequenceParser::getNameMap(string g, string filename){ 
+       try {
+               map<string, map<string, string> >::iterator it;
+               map<string, string> nameMapForThisGroup;
+               
+               it = nameMapPerGroup.find(g);
+               if(it == nameMapPerGroup.end()) {
+                       m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
+               }else {
+                       nameMapForThisGroup = it->second;
+                       
+                       ofstream out;
+                       m->openOutputFile(filename, out);
+                       
+                       for (map<string, string>::iterator itFile = nameMapForThisGroup.begin(); itFile != nameMapForThisGroup.end(); itFile++) {
+                               
+                               if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
+                               
+                               out << itFile->first << '\t' << itFile->second << endl;
+                       }
+                       
+                       out.close();
+               }
+               
+               return 0; 
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SequenceParser", "getNameMap");
+               exit(1);
+       }
+}
+/************************************************************/