*/
#include "mothur.h"
#include "command.hpp"
+#include "sequence.hpp"
class ScreenSeqsCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "screen.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
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 int start;
- unsigned long int end;
- linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
- vector<int> processIDS; //processid
- vector<linePair*> lines;
+ vector<linePair> lines;
- int screenNameGroupFile(set<string>);
- int screenGroupFile(set<string>);
- int screenAlignReport(set<string>);
- int screenQual(set<string>);
-
- int driver(linePair*, string, string, string, set<string>&);
- int createProcesses(string, string, string, set<string>&);
+ int screenNameGroupFile(map<string, string>);
+ int screenGroupFile(map<string, string>);
+ int screenCountFile(map<string, string>);
+ int screenAlignReport(map<string, string>&);
+ int screenQual(map<string, string>);
+ int screenTaxonomy(map<string, string>);
+ int optimizeContigs();
+ int optimizeAlign();
+ int driver(linePair, string, string, string, map<string, string>&);
+ int createProcesses(string, string, string, map<string, string>&);
+ int screenSummary(map<string, string>&);
+ int screenContigs(map<string, string>&);
+ int runFastaScreening(map<string, string>&);
+ int screenFasta(map<string, string>&);
+ int screenReports(map<string, string>&);
+ int getSummary(vector<unsigned long long>&);
+ int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair);
+ int getSummaryReport();
+ int driverContigsSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, linePair);
+ int createProcessesContigsSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<linePair>);
+ int driverAlignSummary(vector<float>&, vector<float>&, vector<int>&, linePair);
+ int createProcessesAlignSummary(vector<float>&, vector<float>&, vector<int>&, vector<linePair>);
+
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, map<string, string>&);
#endif
bool abort;
- string fastafile, namefile, groupfile, alignreport, outputDir, qualfile;
- int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
+ string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile, contigsreport, summaryfile;
+ int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria, minOverlap, oStart, oEnd, mismatches, maxN, maxInsert;
+ float minSim, minScore;
vector<string> outputNames;
vector<string> optimize;
map<string, int> nameMap;
- int readNames();
- int getSummary(vector<unsigned long int>&);
- 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;
+ vector<int> numNs;
+ string filename, namefile, countfile;
+ 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, string cf, map<string, int> nam) {
+ filename = f;
+ namefile = nf;
+ countfile = cf;
+ 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 contigsSumData {
+ vector<int> ostartPosition;
+ vector<int> oendPosition;
+ vector<int> oLength;
+ vector<int> omismatches;
+ vector<int> numNs;
+ string filename, namefile, countfile;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ map<string, int> nameMap;
+
+
+ contigsSumData(){}
+ contigsSumData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string nf, string cf, map<string, int> nam) {
+ filename = f;
+ namefile = nf;
+ countfile = cf;
+ m = mout;
+ start = st;
+ end = en;
+ nameMap = nam;
+ count = 0;
+ }
+};
+/**************************************************************************************************/
+struct alignsData {
+ vector<float> sims;
+ vector<float> scores;
+ vector<int> inserts;
+ string filename, namefile, countfile;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ map<string, int> nameMap;
+
+
+ alignsData(){}
+ alignsData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string nf, string cf, map<string, int> nam) {
+ filename = f;
+ namefile = nf;
+ countfile = cf;
+ 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, maxN;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ string goodFName, badAccnosFName, filename;
+ map<string, string> badSeqNames;
+ string summaryfile, contigsreport;
+
+
+ sumScreenData(){}
+ sumScreenData(int s, int e, int a, int h, int minl, int maxl, int mn, map<string, string> bs, string f, string sum, string cont, 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;
+ maxN = mn;
+ filename = f;
+ goodFName = gf;
+ badAccnosFName = bf;
+ m = mout;
+ start = st;
+ end = en;
+ summaryfile = sum;
+ contigsreport = cont;
+ badSeqNames = bs;
+ 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);
+ }
+
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ 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 != "") || (pDataArray->countfile !="")){
+ //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
+ int numns = current.getNumNs();
+ 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());
+ pDataArray->numNs.push_back(numns);
+ }
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumThreadFunction");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+static DWORD WINAPI MyContigsSumThreadFunction(LPVOID lpParam){
+ contigsSumData* pDataArray;
+ pDataArray = (contigsSumData*)lpParam;
+
+ try {
+ string name;
+ //Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns
+ int length, OLength, thisOStart, thisOEnd, numMisMatches, numns;
+
+ 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); pDataArray->m->getline(in); pDataArray->m->gobble(in);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numns; pDataArray->m->gobble(in);
+
+ int num = 1;
+ if ((pDataArray->namefile != "") || (pDataArray->countfile !="")){
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = pDataArray->nameMap.find(name);
+
+ if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + name + " 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->ostartPosition.push_back(thisOStart);
+ pDataArray->oendPosition.push_back(thisOEnd);
+ pDataArray->oLength.push_back(OLength);
+ pDataArray->omismatches.push_back(numMisMatches);
+ pDataArray->numNs.push_back(numns);
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MyContigsThreadFunction");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+static DWORD WINAPI MyAlignsThreadFunction(LPVOID lpParam){
+ alignsData* pDataArray;
+ pDataArray = (alignsData*)lpParam;
+
+ try {
+
+ string name, TemplateName, SearchMethod, AlignmentMethod;
+ //QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
+ //checking for minScore, maxInsert, minSim
+ int length, TemplateLength, QueryStart, QueryEnd, TemplateStart, TemplateEnd, PairwiseAlignmentLength, GapsInQuery, GapsInTemplate, LongestInsert;
+ float SearchScore, SimBtwnQueryTemplate;
+
+ 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); pDataArray->m->getline(in); pDataArray->m->gobble(in);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ in >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; pDataArray->m->gobble(in);
+ cout << i << '\t' << name << endl;
+ int num = 1;
+ if ((pDataArray->namefile != "") || (pDataArray->countfile !="")){
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = pDataArray->nameMap.find(name);
+
+ if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + name + " 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->sims.push_back(SimBtwnQueryTemplate);
+ pDataArray->scores.push_back(SearchScore);
+ pDataArray->inserts.push_back(LongestInsert);
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MyAlignsThreadFunction");
+ 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);
+ }
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ 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
+ string trashCode = "";
+ //have the report files found you bad
+ map<string, string>::iterator it = pDataArray->badSeqNames.find(currSeq.getName());
+ if (it != pDataArray->badSeqNames.end()) { goodSeq = 0; trashCode = it->second; } //found it
+
+ if (pDataArray->summaryfile == "") {
+ if(pDataArray->startPos != -1 && pDataArray->startPos < currSeq.getStartPos()) { goodSeq = 0; trashCode += "start|"; }
+ if(pDataArray->endPos != -1 && pDataArray->endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|"; }
+ if(pDataArray->maxAmbig != -1 && pDataArray->maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|"; }
+ if(pDataArray->maxHomoP != -1 && pDataArray->maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|"; }
+ if(pDataArray->minLength != -1 && pDataArray->minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|"; }
+ if(pDataArray->maxLength != -1 && pDataArray->maxLength < currSeq.getNumBases()) { goodSeq = 0; trashCode += ">length|"; }
+ }
+ if (pDataArray->contigsreport == "") { //contigs report includes this so no need to check again
+ if(pDataArray->maxN != -1 && pDataArray->maxN < currSeq.getNumNs()) { goodSeq = 0; trashCode += "n|"; }
+ }
+
+
+ if(goodSeq == 1){
+ currSeq.printSequence(goodFile);
+ }
+ else{
+ badAccnosFile << currSeq.getName() << '\t' << trashCode.substr(0, trashCode.length()-1) << endl;
+ pDataArray->badSeqNames[currSeq.getName()] = trashCode;
+ }
+
+ }
+ //report progress
+ if((i+1) % 100 == 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(i+1)+"\n"); }
+ }
+ //report progress
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n"); }
+
+
+
+ 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