X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequenceparser.cpp;h=fd94b246a43217cc9cbfa131bfe4cd672955e001;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=44012d8ba8321fea520fbe613e0dac8f8911c760;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index 44012d8..fd94b24 100644
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -7,7 +7,7 @@
  *
  */
 
-#include "sequenceParser.h"
+#include "sequenceparser.h"
 
 
 /************************************************************/
@@ -63,6 +63,8 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 		
 		string first, second;
 		int countName = 0;
+		set<string> thisnames1;
+		
 		while(!inName.eof()) {
 			
 			if (m->control_pressed) { break; }
@@ -94,10 +96,12 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 					it = splitMap.find(group);
 					if (it != splitMap.end()) { //adding seqs to this group
 						(it->second) += "," + names[i];
+						thisnames1.insert(names[i]);
 						countName++;
 					}else { //first sighting of this group
 						splitMap[group] = names[i];
 						countName++;
+						thisnames1.insert(names[i]);
 						
 						//is this seq in the fasta file?
 						if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
@@ -106,6 +110,8 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 						}
 					}
 				}
+				
+				allSeqsMap[names[i]] = names[0];
 			}
 			
 			
@@ -129,6 +135,15 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 		if (error == 1) { m->control_pressed = true; }
 		
 		if (countName != (groupMap->getNumSeqs())) {
+			vector<string> groupseqsnames = groupMap->getNamesSeqs();
+			
+			for (int i = 0; i < groupseqsnames.size(); i++) {
+				set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
+				if (itnamesfile == thisnames1.end()){
+					cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
+				}
+			}
+			
 			m->mothurOutEndLine();
 			m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 			m->mothurOutEndLine();
@@ -247,6 +262,79 @@ 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 { 
+                //m->mothurOut("Group " + g +  " contains " + toString(seqForThisGroup.size()) + " unique seqs.\n");
+				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 +356,38 @@ 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);
+	}
+}
+/************************************************************/