+++ /dev/null
-#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
projects / mothur.git / blobdiff