int SeqSummaryCommand::execute(){ try{ if (abort == true) { if (calledHelp) { return 0; } return 2; } //set current fasta to fastafile m->setFastaFile(fastafile); map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); string summaryFile = getOutputFileName("summary",variables); int numSeqs = 0; vector<int> startPosition; vector<int> endPosition; vector<int> seqLength; vector<int> ambigBases; vector<int> longHomoPolymer; if (namefile != "") { nameMap = m->readNames(namefile); } else if (countfile != "") { CountTable ct; ct.readTable(countfile, false, false); nameMap = ct.getNameMap(); } if (m->control_pressed) { return 0; } #ifdef USE_MPI int pid, numSeqsPerProcessor; int tag = 2001; int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5; int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; vector<unsigned long long> MPIPos; MPI_Status status; MPI_Status statusOut; MPI_File inMPI; MPI_File outMPI; MPI_Comm_size(MPI_COMM_WORLD, &processors); MPI_Comm_rank(MPI_COMM_WORLD, &pid); char tempFileName[1024]; strcpy(tempFileName, fastafile.c_str()); char sumFileName[1024]; strcpy(sumFileName, summaryFile.c_str()); MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI); if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } if (pid == 0) { //you are the root process //print header string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n"; int length = outputString.length(); char* buf2 = new char[length]; memcpy(buf2, outputString.c_str(), length); MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut); delete buf2; MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs for(int i = 1; i < processors; i++) { MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); } //figure out how many sequences you have to do numSeqsPerProcessor = numSeqs / processors; int startIndex = pid * numSeqsPerProcessor; if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } //do your part MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos); }else { //i am the child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); MPIPos.resize(numSeqs+1); MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); //figure out how many sequences you have to align numSeqsPerProcessor = numSeqs / processors; int startIndex = pid * numSeqsPerProcessor; if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } //do your part MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos); } MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case if (pid == 0) { //get the info from the child processes for(int i = 1; i < processors; i++) { int size; MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); vector<int> temp; temp.resize(size+1); for(int j = 0; j < 5; j++) { MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status); int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what count this is for if (receiveTag == startTag) { for (int k = 0; k < size; k++) { startPosition.push_back(temp[k]); } }else if (receiveTag == endTag) { for (int k = 0; k < size; k++) { endPosition.push_back(temp[k]); } }else if (receiveTag == lengthTag) { for (int k = 0; k < size; k++) { seqLength.push_back(temp[k]); } }else if (receiveTag == baseTag) { for (int k = 0; k < size; k++) { ambigBases.push_back(temp[k]); } }else if (receiveTag == lhomoTag) { for (int k = 0; k < size; k++) { longHomoPolymer.push_back(temp[k]); } } } } }else{ //send my counts int size = startPosition.size(); MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); startPosition.push_back(startTag); int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); endPosition.push_back(endTag); ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); seqLength.push_back(lengthTag); ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); ambigBases.push_back(baseTag); ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); longHomoPolymer.push_back(lhomoTag); ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD); } MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else vector<unsigned long long> positions; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) positions = m->divideFile(fastafile, processors); for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); } #else positions = m->setFilePosFasta(fastafile, numSeqs); if (positions.size() < processors) { processors = positions.size(); } //figure out how many sequences you have to process int numSeqsPerProcessor = numSeqs / processors; for (int i = 0; i < processors; i++) { int startIndex = i * numSeqsPerProcessor; if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; } lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor)); } #endif if(processors == 1){ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]); }else{ numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile); } if (m->control_pressed) { return 0; } #endif #ifdef USE_MPI if (pid == 0) { #endif sort(startPosition.begin(), startPosition.end()); sort(endPosition.begin(), endPosition.end()); sort(seqLength.begin(), seqLength.end()); sort(ambigBases.begin(), ambigBases.end()); sort(longHomoPolymer.begin(), longHomoPolymer.end()); int size = startPosition.size(); //find means unsigned long long meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer; meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0; for (int i = 0; i < size; i++) { meanStartPosition += startPosition[i]; meanEndPosition += endPosition[i]; meanSeqLength += seqLength[i]; meanAmbigBases += ambigBases[i]; meanLongHomoPolymer += longHomoPolymer[i]; } double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer; meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size; int ptile0_25 = int(size * 0.025); int ptile25 = int(size * 0.250); int ptile50 = int(size * 0.500); int ptile75 = int(size * 0.750); int ptile97_5 = int(size * 0.975); int ptile100 = size - 1; //to compensate for blank sequences that would result in startPosition and endPostion equalling -1 if (startPosition[0] == -1) { startPosition[0] = 0; } if (endPosition[0] == -1) { endPosition[0] = 0; } if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } m->mothurOutEndLine(); m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine(); m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0]) + "\t" + toString(1)); m->mothurOutEndLine(); m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25]) + "\t" + toString(ptile0_25+1)); m->mothurOutEndLine(); m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25]) + "\t" + toString(ptile25+1)); m->mothurOutEndLine(); m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50]) + "\t" + toString(ptile50+1)); m->mothurOutEndLine(); m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine(); m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine(); m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine(); m->mothurOut("Mean:\t" + toString(meanstartPosition) + "\t" + toString(meanendPosition) + "\t" + toString(meanseqLength) + "\t" + toString(meanambigBases) + "\t" + toString(meanlongHomoPolymer)); m->mothurOutEndLine(); if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); } else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); } if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile); m->mothurOutEndLine(); #ifdef USE_MPI } #endif //set fasta file as new current fastafile string current = ""; itTypes = outputTypes.find("summary"); if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); } } return 0; } catch(exception& e) { m->errorOut(e, "SeqSummaryCommand", "execute"); exit(1); } }
//*************************************************************************************************************** int SummaryQualCommand::execute(){ try{ if (abort == true) { if (calledHelp) { return 0; } return 2; } int start = time(NULL); int numSeqs = 0; vector<int> position; vector<int> averageQ; vector< vector<int> > scores; if (m->control_pressed) { return 0; } if (namefile != "") { nameMap = m->readNames(namefile); } else if (countfile != "") { CountTable ct; ct.readTable(countfile, false, false); nameMap = ct.getNameMap(); } vector<unsigned long long> positions; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) positions = m->divideFile(qualfile, processors); for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); } #else if (processors == 1) { lines.push_back(linePair(0, 1000)); }else { positions = m->setFilePosFasta(qualfile, numSeqs); if (numSeqs < processors) { processors = numSeqs; } //figure out how many sequences you have to process int numSeqsPerProcessor = numSeqs / processors; for (int i = 0; i < processors; i++) { int startIndex = i * numSeqsPerProcessor; if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; } lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor)); } } #endif if(processors == 1){ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]); } else{ numSeqs = createProcessesCreateSummary(position, averageQ, scores, qualfile); } if (m->control_pressed) { return 0; } //print summary file map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile)); string summaryFile = getOutputFileName("summary",variables); printQual(summaryFile, position, averageQ, scores); if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } //output results to screen cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint); m->mothurOutEndLine(); m->mothurOut("Position\tNumSeqs\tAverageQ"); m->mothurOutEndLine(); for (int i = 0; i < position.size(); i+=100) { float average = averageQ[i] / (float) position[i]; cout << i << '\t' << position[i] << '\t' << average; m->mothurOutJustToLog(toString(i) + "\t" + toString(position[i]) + "\t" + toString(average)); m->mothurOutEndLine(); } m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile); m->mothurOutEndLine(); return 0; } catch(exception& e) { m->errorOut(e, "SummaryQualCommand", "execute"); exit(1); } }
int SeqSummaryCommand::execute(){ try{ if (abort == true) { if (calledHelp) { return 0; } return 2; } int start = time(NULL); //set current fasta to fastafile m->setFastaFile(fastafile); map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); string summaryFile = getOutputFileName("summary",variables); long long numSeqs = 0; long long size = 0; long long numUniques = 0; map<int, long long> startPosition; map<int, long long> endPosition; map<int, long long> seqLength; map<int, long long> ambigBases; map<int, long long> longHomoPolymer; if (namefile != "") { nameMap = m->readNames(namefile); numUniques = nameMap.size(); } else if (countfile != "") { CountTable ct; ct.readTable(countfile, false, false); nameMap = ct.getNameMap(); size = ct.getNumSeqs(); numUniques = ct.getNumUniqueSeqs(); } if (m->control_pressed) { return 0; } vector<unsigned long long> positions; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) positions = m->divideFile(fastafile, processors); for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); } #else positions = m->setFilePosFasta(fastafile, numSeqs); if (numSeqs < processors) { processors = numSeqs; } //figure out how many sequences you have to process int numSeqsPerProcessor = numSeqs / processors; for (int i = 0; i < processors; i++) { int startIndex = i * numSeqsPerProcessor; if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; } lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor)); } #endif if(processors == 1){ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]); }else{ numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile); } if (m->control_pressed) { return 0; } //set size if (countfile != "") {}//already set else if (namefile == "") { size = numSeqs; } else { for (map<int, long long>::iterator it = startPosition.begin(); it != startPosition.end(); it++) { size += it->second; } } if ((namefile != "") || (countfile != "")) { string type = "count"; if (namefile != "") { type = "name"; } if (numSeqs != numUniques) { // do fasta and name/count files match m->mothurOut("[ERROR]: Your " + type + " file contains " + toString(numUniques) + " unique sequences, but your fasta file contains " + toString(numSeqs) + ". File mismatch detected, quitting command.\n"); m->control_pressed = true; } } if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } long long ptile0_25 = 1+(long long)(size * 0.025); //number of sequences at 2.5% long long ptile25 = 1+(long long)(size * 0.250); //number of sequences at 25% long long ptile50 = 1+(long long)(size * 0.500); long long ptile75 = 1+(long long)(size * 0.750); long long ptile97_5 = 1+(long long)(size * 0.975); long long ptile100 = (long long)(size); vector<int> starts; starts.resize(7,0); vector<int> ends; ends.resize(7,0); vector<int> ambigs; ambigs.resize(7,0); vector<int> lengths; lengths.resize(7,0); vector<int> homops; homops.resize(7,0); //find means long long meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer; meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0; //minimum if ((startPosition.begin())->first == -1) { starts[0] = 0; } else {starts[0] = (startPosition.begin())->first; } long long totalSoFar = 0; //set all values to min starts[1] = starts[0]; starts[2] = starts[0]; starts[3] = starts[0]; starts[4] = starts[0]; starts[5] = starts[0]; int lastValue = 0; for (map<int, long long>::iterator it = startPosition.begin(); it != startPosition.end(); it++) { int value = it->first; if (value == -1) { value = 0; } meanStartPosition += (value*it->second); totalSoFar += it->second; if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ starts[1] = value; } //save value if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { starts[2] = value; } //save value if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { starts[3] = value; } //save value if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { starts[4] = value; } //save value if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { starts[5] = value; } //save value if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { starts[6] = value; } //save value lastValue = totalSoFar; } starts[6] = (startPosition.rbegin())->first; if ((endPosition.begin())->first == -1) { ends[0] = 0; } else {ends[0] = (endPosition.begin())->first; } totalSoFar = 0; //set all values to min ends[1] = ends[0]; ends[2] = ends[0]; ends[3] = ends[0]; ends[4] = ends[0]; ends[5] = ends[0]; lastValue = 0; for (map<int, long long>::iterator it = endPosition.begin(); it != endPosition.end(); it++) { int value = it->first; if (value == -1) { value = 0; } meanEndPosition += (value*it->second); totalSoFar += it->second; if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ ends[1] = value; } //save value if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { ends[2] = value; } //save value if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { ends[3] = value; } //save value if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { ends[4] = value; } //save value if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { ends[5] = value; } //save value if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { ends[6] = value; } //save value lastValue = totalSoFar; } ends[6] = (endPosition.rbegin())->first; if ((seqLength.begin())->first == -1) { lengths[0] = 0; } else {lengths[0] = (seqLength.begin())->first; } //set all values to min lengths[1] = lengths[0]; lengths[2] = lengths[0]; lengths[3] = lengths[0]; lengths[4] = lengths[0]; lengths[5] = lengths[0]; totalSoFar = 0; lastValue = 0; for (map<int, long long>::iterator it = seqLength.begin(); it != seqLength.end(); it++) { int value = it->first; meanSeqLength += (value*it->second); totalSoFar += it->second; if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ lengths[1] = value; } //save value if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { lengths[2] = value; } //save value if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { lengths[3] = value; } //save value if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { lengths[4] = value; } //save value if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { lengths[5] = value; } //save value if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { lengths[6] = value; } //save value lastValue = totalSoFar; } lengths[6] = (seqLength.rbegin())->first; if ((ambigBases.begin())->first == -1) { ambigs[0] = 0; } else {ambigs[0] = (ambigBases.begin())->first; } //set all values to min ambigs[1] = ambigs[0]; ambigs[2] = ambigs[0]; ambigs[3] = ambigs[0]; ambigs[4] = ambigs[0]; ambigs[5] = ambigs[0]; totalSoFar = 0; lastValue = 0; for (map<int, long long>::iterator it = ambigBases.begin(); it != ambigBases.end(); it++) { int value = it->first; meanAmbigBases += (value*it->second); totalSoFar += it->second; if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ ambigs[1] = value; } //save value if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { ambigs[2] = value; } //save value if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { ambigs[3] = value; } //save value if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { ambigs[4] = value; } //save value if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { ambigs[5] = value; } //save value if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { ambigs[6] = value; } //save value lastValue = totalSoFar; } ambigs[6] = (ambigBases.rbegin())->first; if ((longHomoPolymer.begin())->first == -1) { homops[0] = 0; } else {homops[0] = (longHomoPolymer.begin())->first; } //set all values to min homops[1] = homops[0]; homops[2] = homops[0]; homops[3] = homops[0]; homops[4] = homops[0]; homops[5] = homops[0]; totalSoFar = 0; lastValue = 0; for (map<int, long long>::iterator it = longHomoPolymer.begin(); it != longHomoPolymer.end(); it++) { int value = it->first; meanLongHomoPolymer += (it->first*it->second); totalSoFar += it->second; if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ homops[1] = value; } //save value if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { homops[2] = value; } //save value if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { homops[3] = value; } //save value if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { homops[4] = value; } //save value if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { homops[5] = value; } //save value if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { homops[6] = value; } //save value lastValue = totalSoFar; } homops[6] = (longHomoPolymer.rbegin())->first; double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer; meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size; if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } m->mothurOutEndLine(); m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine(); m->mothurOut("Minimum:\t" + toString(starts[0]) + "\t" + toString(ends[0]) + "\t" + toString(lengths[0]) + "\t" + toString(ambigs[0]) + "\t" + toString(homops[0]) + "\t" + toString(1)); m->mothurOutEndLine(); m->mothurOut("2.5%-tile:\t" + toString(starts[1]) + "\t" + toString(ends[1]) + "\t" + toString(lengths[1]) + "\t" + toString(ambigs[1]) + "\t" + toString(homops[1]) + "\t" + toString(ptile0_25)); m->mothurOutEndLine(); m->mothurOut("25%-tile:\t" + toString(starts[2]) + "\t" + toString(ends[2]) + "\t" + toString(lengths[2]) + "\t" + toString(ambigs[2]) + "\t" + toString(homops[2]) + "\t" + toString(ptile25)); m->mothurOutEndLine(); m->mothurOut("Median: \t" + toString(starts[3]) + "\t" + toString(ends[3]) + "\t" + toString(lengths[3]) + "\t" + toString(ambigs[3]) + "\t" + toString(homops[3]) + "\t" + toString(ptile50)); m->mothurOutEndLine(); m->mothurOut("75%-tile:\t" + toString(starts[4]) + "\t" + toString(ends[4]) + "\t" + toString(lengths[4]) + "\t" + toString(ambigs[4]) + "\t" + toString(homops[4]) + "\t" + toString(ptile75)); m->mothurOutEndLine(); m->mothurOut("97.5%-tile:\t" + toString(starts[5]) + "\t" + toString(ends[5]) + "\t" + toString(lengths[5]) + "\t" + toString(ambigs[5]) + "\t" + toString(homops[5]) + "\t" + toString(ptile97_5)); m->mothurOutEndLine(); m->mothurOut("Maximum:\t" + toString(starts[6]) + "\t" + toString(ends[6]) + "\t" + toString(lengths[6]) + "\t" + toString(ambigs[6]) + "\t" + toString(homops[6]) + "\t" + toString(ptile100)); m->mothurOutEndLine(); m->mothurOut("Mean:\t" + toString(meanstartPosition) + "\t" + toString(meanendPosition) + "\t" + toString(meanseqLength) + "\t" + toString(meanambigBases) + "\t" + toString(meanlongHomoPolymer)); m->mothurOutEndLine(); if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); } else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); } if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile); m->mothurOutEndLine(); if ((namefile == "") && (countfile == "")) { m->mothurOut("It took " + toString(time(NULL) - start) + " secs to summarize " + toString(numSeqs) + " sequences.\n"); } else{ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to summarize " + toString(size) + " sequences.\n"); } //set fasta file as new current fastafile string current = ""; itTypes = outputTypes.find("summary"); if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); } } return 0; } catch(exception& e) { m->errorOut(e, "SeqSummaryCommand", "execute"); exit(1); } }