X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;fp=screenseqscommand.h;h=291d8e6d1acd4605f4827159f10aa74269e1a771;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
new file mode 100644
index 0000000..291d8e6
--- /dev/null
+++ b/screenseqscommand.h
@@ -0,0 +1,266 @@
+#ifndef SCREENSEQSCOMMAND_H
+#define SCREENSEQSCOMMAND_H
+
+/*
+ *  screenseqscommand.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 6/3/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+#include "mothur.h"
+#include "command.hpp"
+#include "sequence.hpp"
+
+class ScreenSeqsCommand : public Command {
+	
+public:
+	ScreenSeqsCommand(string);
+	ScreenSeqsCommand();
+	~ScreenSeqsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "screen.seqs";				}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
+	string getDescription()		{ return "enables you to keep sequences that fulfill certain user defined criteria"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
+private:
+
+	struct linePair {
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+	};
+
+	vector<linePair> lines;
+
+	int screenNameGroupFile(set<string>);
+	int screenGroupFile(set<string>);
+	int screenAlignReport(set<string>);
+	int screenQual(set<string>);
+	int screenTaxonomy(set<string>);
+	
+	int driver(linePair, string, string, string, set<string>&);
+	int createProcesses(string, string, string, set<string>&);
+	
+	#ifdef USE_MPI
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, set<string>&);
+	#endif
+
+	bool abort;
+	string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
+	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
+	vector<string> outputNames;
+	vector<string> optimize;
+	map<string, int> nameMap;
+	int readNames();
+	
+	int getSummary(vector<unsigned long long>&);
+	int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+	int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair);	
+};
+
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct sumData {
+	vector<int> startPosition;
+	vector<int> endPosition;
+	vector<int> seqLength; 
+	vector<int> ambigBases; 
+	vector<int> longHomoPolymer; 
+	string filename, namefile; 
+	unsigned long long start;
+	unsigned long long end;
+	int count;
+	MothurOut* m;
+	map<string, int> nameMap;
+	
+	
+	sumData(){}
+	sumData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string nf, map<string, int> nam) {
+		filename = f;
+        namefile = nf;
+		m = mout;
+		start = st;
+		end = en;
+		nameMap = nam;
+		count = 0;
+	}
+};
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct sumScreenData {
+    int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
+	unsigned long long start;
+	unsigned long long end;
+	int count;
+	MothurOut* m;
+	string goodFName, badAccnosFName, filename;
+    set<string> badSeqNames;
+	
+	
+	sumScreenData(){}
+	sumScreenData(int s, int e, int a, int h, int minl, int maxl, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string gf, string bf) {
+		startPos = s;
+		endPos = e;
+		minLength = minl;
+        maxLength = maxl;
+		maxAmbig = a;
+		maxHomoP = h;
+		filename = f;
+        goodFName = gf;
+        badAccnosFName = bf;
+		m = mout;
+		start = st;
+		end = en;
+		count = 0;
+	}
+};
+
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MySumThreadFunction(LPVOID lpParam){ 
+	sumData* pDataArray;
+	pDataArray = (sumData*)lpParam;
+	
+	try {
+		ifstream in;
+		pDataArray->m->openInputFile(pDataArray->filename, in);
+        
+		//print header if you are process 0
+		if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+			in.seekg(0);
+		}else { //this accounts for the difference in line endings. 
+			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
+		}
+		
+		pDataArray->count = pDataArray->end;
+		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+			
+			if (pDataArray->m->control_pressed) { in.close();  pDataArray->count = 1; return 1; }
+			
+			Sequence current(in); pDataArray->m->gobble(in); 
+			
+			if (current.getName() != "") {
+				
+				int num = 1;
+				if (pDataArray->namefile != "") {
+					//make sure this sequence is in the namefile, else error 
+					map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
+					
+					if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+					else { num = it->second; }
+				}
+				
+				//for each sequence this sequence represents
+				for (int i = 0; i < num; i++) {
+					pDataArray->startPosition.push_back(current.getStartPos());
+					pDataArray->endPosition.push_back(current.getEndPos());
+					pDataArray->seqLength.push_back(current.getNumBases());
+					pDataArray->ambigBases.push_back(current.getAmbigBases());
+					pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
+				}
+            }
+		}
+		
+		in.close();
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumThreadFunction");
+		exit(1);
+	}
+} 
+
+/**************************************************************************************************/
+
+static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){ 
+	sumScreenData* pDataArray;
+	pDataArray = (sumScreenData*)lpParam;
+	
+	try {
+        
+        ofstream goodFile;
+		pDataArray->m->openOutputFile(pDataArray->goodFName, goodFile);
+		
+		ofstream badAccnosFile;
+		pDataArray->m->openOutputFile(pDataArray->badAccnosFName, badAccnosFile);
+		
+		ifstream in;
+		pDataArray->m->openInputFile(pDataArray->filename, in);
+        
+		//print header if you are process 0
+		if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+			in.seekg(0);
+		}else { //this accounts for the difference in line endings. 
+			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
+		}
+		
+		pDataArray->count = pDataArray->end;
+		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+			
+			if (pDataArray->m->control_pressed) { in.close(); badAccnosFile.close(); goodFile.close(); pDataArray->count = 1; return 1; }
+			
+			Sequence currSeq(in); pDataArray->m->gobble(in); 
+			
+			if (currSeq.getName() != "") {
+				bool goodSeq = 1;		//	innocent until proven guilty
+				if(goodSeq == 1 && pDataArray->startPos != -1 && pDataArray->startPos < currSeq.getStartPos())			{	goodSeq = 0;	}
+				if(goodSeq == 1 && pDataArray->endPos != -1 && pDataArray->endPos > currSeq.getEndPos())				{	goodSeq = 0;	}
+				if(goodSeq == 1 && pDataArray->maxAmbig != -1 && pDataArray->maxAmbig <	currSeq.getAmbigBases())		{	goodSeq = 0;	}
+				if(goodSeq == 1 && pDataArray->maxHomoP != -1 && pDataArray->maxHomoP < currSeq.getLongHomoPolymer())	{	goodSeq = 0;	}
+				if(goodSeq == 1 && pDataArray->minLength != -1 && pDataArray->minLength > currSeq.getNumBases())		{	goodSeq = 0;	}
+				if(goodSeq == 1 && pDataArray->maxLength != -1 && pDataArray->maxLength < currSeq.getNumBases())		{	goodSeq = 0;	}
+				
+				if(goodSeq == 1){
+					currSeq.printSequence(goodFile);	
+				}
+				else{
+					badAccnosFile << currSeq.getName() << endl;
+					pDataArray->badSeqNames.insert(currSeq.getName());
+				}
+    
+			}		
+            //report progress
+			if((i+1) % 100 == 0){	pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine();		}
+		}
+		//report progress
+		if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
+		
+
+		
+		in.close();
+        goodFile.close();
+        badAccnosFile.close();
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumScreenThreadFunction");
+		exit(1);
+	}
+} 
+
+#endif
+
+/**************************************************************************************************/
+
+
+
+#endif