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#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, set<string>* bn) {
startPos = s;
endPos = e;
minLength = minl;
maxLength = maxl;
maxAmbig = a;
maxHomoP = h;
filename = f;
goodFName = gf;
badAccnosFName = bf;
m = mout;
start = st;
end = en;
badSeqNames = bn;
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
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