#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
+#include "sequence.hpp"
-using namespace std;
+/**************************************************************************************************/
class SeqSummaryCommand : public Command {
public:
+ SeqSummaryCommand(string);
SeqSummaryCommand();
- ~SeqSummaryCommand();
- int execute();
+ ~SeqSummaryCommand(){}
+ vector<string> setParameters();
+ string getCommandName() { return "summary.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
+ string getDescription() { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
+ bool abort;
+ string fastafile, outputDir, namefile, countfile;
+ int processors;
+ vector<string> outputNames;
+ map<string, int> nameMap;
+
+ 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;
+ vector<int> processIDS;
+
+ int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
+
+ #ifdef USE_MPI
+ int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long long>&);
+ #endif
+
+};
+
+/**************************************************************************************************/
+//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 seqSumData {
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
+ string filename;
+ string sumFile;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ bool hasNameMap;
+ map<string, int> nameMap;
+
+
+ seqSumData(){}
+ seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, bool na, map<string, int> nam) {
+ filename = f;
+ sumFile = sf;
+ m = mout;
+ start = st;
+ end = en;
+ hasNameMap = na;
+ nameMap = nam;
+ count = 0;
+ }
};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
+ seqSumData* pDataArray;
+ pDataArray = (seqSumData*)lpParam;
+
+ try {
+ ofstream outSummary;
+ pDataArray->m->openOutputFile(pDataArray->sumFile, outSummary);
+
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
+ 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(); outSummary.close(); pDataArray->count = 1; return 1; }
+
+ Sequence current(in); pDataArray->m->gobble(in);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if (pDataArray->hasNameMap){
+ //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 name or count file, 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());
+ }
+
+ outSummary << current.getName() << '\t';
+ outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
+ outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
+ outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+ }
+ }
+
+ in.close();
+ outSummary.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "SeqSummaryCommand", "MySeqSumThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+
+
+
#endif
+
+/**************************************************************************************************/
+
+
projects / mothur.git / blobdiff