#include "screenseqscommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> ScreenSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "start", "end", "maxambig", "maxhomop","optimize","criteria", "minlength", "maxlength",
+ "name", "group", "alignreport","processors","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ScreenSeqsCommand::ScreenSeqsCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ScreenSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ScreenSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(string option) {
else {
//valid paramters for this command
- string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
+ string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop","optimize","criteria", "minlength", "maxlength",
"name", "group", "alignreport","processors","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
convert(temp, processors);
-
+
+ temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
+ if (temp == "not found"){ temp = ""; }
+ else { m->splitAtDash(temp, optimize); }
+
+ //check for invalid optimize options
+ set<string> validOptimizers;
+ validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
+
+ for (int i = 0; i < optimize.size(); i++) {
+ if (validOptimizers.count(optimize[i]) == 0) {
+ m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
+ optimize.erase(optimize.begin()+i);
+ i--;
+ }
+ }
+
+ temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){ temp = "90"; }
+ convert(temp, criteria);
}
}
void ScreenSeqsCommand::help(){
try {
m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
- m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group and processors.\n");
+ m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, optimize, criteria and processors.\n");
m->mothurOut("The fasta parameter is required.\n");
m->mothurOut("The start parameter .... The default is -1.\n");
m->mothurOut("The end parameter .... The default is -1.\n");
m->mothurOut("The minlength parameter .... The default is -1.\n");
m->mothurOut("The maxlength parameter .... The default is -1.\n");
m->mothurOut("The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n");
+ m->mothurOut("The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n");
+ m->mothurOut("For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n");
m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
m->mothurOut("The screen.seqs command should be in the following format: \n");
m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n");
try{
if (abort == true) { return 0; }
+
+ //if the user want to optimize we need to no the 90% mark
+ vector<unsigned long int> positions;
+ if (optimize.size() != 0) { getSummary(positions); } //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
+ else {
+ positions = m->divideFile(fastafile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+ }
string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
string badAccnosFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long int> positions = m->divideFile(fastafile, processors);
-
- for (int i = 0; i < (positions.size()-1); i++) {
- lines.push_back(new linePair(positions[i], positions[(i+1)]));
- }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(goodSeqFile); m->mothurOutEndLine();
- m->mothurOut(badAccnosFile); m->mothurOutEndLine();
+ m->mothurOut(goodSeqFile); m->mothurOutEndLine(); outputTypes["fasta"].push_back(goodSeqFile);
+ m->mothurOut(badAccnosFile); m->mothurOutEndLine(); outputTypes["accnos"].push_back(badAccnosFile);
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
m->mothurOutEndLine();
set<string>::iterator it;
string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
- outputNames.push_back(goodNameFile);
+ outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile);
ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
m->openInputFile(groupfile, inputGroups);
string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
- outputNames.push_back(goodGroupFile);
+ outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
exit(1);
}
}
+//***************************************************************************************************************
+int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
+ try {
+
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
+
+ vector<unsigned long int> positions = m->divideFile(fastafile, processors);
+
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+
+ int numSeqs = 0;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ }else{
+ numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
+ }
+
+ if (m->control_pressed) { return 0; }
+ #else
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ if (m->control_pressed) { return 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 criteriaPercentile = int(numSeqs * (criteria / (float) 100));
+
+ for (int i = 0; i < optimize.size(); i++) {
+ if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "end") { int endcriteriaPercentile = int(numSeqs * ((100 - criteria) / (float) 100)); endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
+ else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(numSeqs * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
+ try {
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ in.seekg(filePos->start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ Sequence current(in); m->gobble(in);
+
+ if (current.getName() != "") {
+ startPosition.push_back(current.getStartPos());
+ endPosition.push_back(current.getEndPos());
+ seqLength.push_back(current.getNumBases());
+ ambigBases.push_back(current.getAmbigBases());
+ longHomoPolymer.push_back(current.getLongHomoPolymer());
+ count++;
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long int pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+ if (in.eof()) { break; }
+ #endif
+
+ }
+
+ in.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ processIDS.clear();
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = fastafile + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << num << endl;
+ for (int k = 0; k < startPosition.size(); k++) { out << startPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < endPosition.size(); k++) { out << endPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < seqLength.size(); k++) { out << seqLength[k] << '\t'; } out << endl;
+ for (int k = 0; k < ambigBases.size(); k++) { out << ambigBases[k] << '\t'; } out << endl;
+ for (int k = 0; k < longHomoPolymer.size(); k++) { out << longHomoPolymer[k] << '\t'; } out << endl;
+
+ out.close();
+
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }
+
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
+
+ int temp, tempNum;
+ in >> tempNum; m->gobble(in); num += tempNum;
+ for (int k = 0; k < tempNum; k++) { in >> temp; startPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; endPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in);
+
+ in.close();
+ remove(tempFilename.c_str());
+ }
+
+ return num;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
+ exit(1);
+ }
+}
//***************************************************************************************************************
set<string>::iterator it;
string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
- outputNames.push_back(goodGroupFile);
+ outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
while(!inputGroups.eof()){
set<string>::iterator it;
string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
- outputNames.push_back(goodAlignReportFile);
+ outputNames.push_back(goodAlignReportFile); outputTypes["alignreport"].push_back(goodAlignReportFile);
ofstream goodAlignReportOut; m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
while (!inputAlignReport.eof()) { // need to copy header
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