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/*
* sffinfocommand.cpp
* Mothur
*
* Created by westcott on 7/7/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "sffinfocommand.h"
#include "endiannessmacros.h"
#include "trimoligos.h"
#include "sequence.hpp"
#include "qualityscores.h"
//**************************************************************************************
vector<string> SffInfoCommand::setParameters(){
try {
CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(psff);
CommandParameter poligos("oligos", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(poligos);
CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
CommandParameter pgroup("group", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(pgroup);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "","",false,false); parameters.push_back(psfftxt);
CommandParameter pflow("flow", "Boolean", "", "T", "", "", "","flow",false,false); parameters.push_back(pflow);
CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
CommandParameter pqfile("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqfile);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
hasAccnos = false; hasOligos = false; hasGroup = false;
split = 1;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["sfftxt"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["sff"] = tempOutNames;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "setParameters");
exit(1);
}
}
//****************************************************************************************
string SffInfoCommand::getHelpString(){
try {
string helpString = "";
helpString += "The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sff file.\n";
helpString += "The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, oligos, group, bdiffs, tdiffs, ldiffs, sdiffs, pdiffs, checkorient and trim. sff is required. \n";
helpString += "The sff parameter allows you to enter the sff file you would like to extract data from.\n";
helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated. Default=True. \n";
helpString += "The qfile parameter allows you to indicate if you would like a quality file generated. Default=True. \n";
helpString += "The oligos parameter allows you to provide an oligos file to split your sff file into separate sff files by barcode. \n";
helpString += "The group parameter allows you to provide a group file to split your sff file into separate sff files by group. \n";
helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. The default is false.\n";
helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated. Default=True. \n";
helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. Default=False. \n";
helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n";
helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. Default=True. \n";
helpString += "The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted.\n";
helpString += "Example sffinfo(sff=mySffFile.sff, trim=F).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "getHelpString");
exit(1);
}
}
//************************************************************************************
string SffInfoCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],fasta-[filename],[tag],fasta"; }
else if (type == "flow") { pattern = "[filename],flow"; }
else if (type == "sfftxt") { pattern = "[filename],sff.txt"; }
else if (type == "sff") { pattern = "[filename],[group],sff"; }
else if (type == "qfile") { pattern = "[filename],qual-[filename],[tag],qual"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "getOutputPattern");
exit(1);
}
}
//*******************************************************************************
SffInfoCommand::SffInfoCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
string inputDir = validParameter.validPath(parameters, "inputdir");
if (inputDir == "not found"){ inputDir = ""; }
sffFilename = validParameter.validFile(parameters, "sff");
if (sffFilename == "not found") {
sffFilename = current->getSFFFile();
if (sffFilename != "") { m->mothurOut("Using " + sffFilename + " as input file for the sff parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current sff file and the sff parameter is required.\n"); abort = true; }
}
else if (sffFilename == "not open") { abort = true; }
else { current->setSFFFile(sffFilename); }
accnosName = validParameter.validFile(parameters, "accnos");
if (accnosName == "not found") { accnosName = ""; }
else if (accnosName == "not open") { accnosName = ""; abort = true; }
else { current->setAccnosFile(accnosName); hasAccnos = true; }
oligosfile = validParameter.validFile(parameters, "oligos");
if (oligosfile == "not found") { oligosfile = ""; }
else if (oligosfile == "not open") { oligosfile = ""; abort = true; }
else { current->setOligosFile(oligosfile); hasOligos = true; }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not found") { groupfile = ""; }
else if (groupfile == "not open") { groupfile = ""; abort = true; }
else { current->setGroupFile(groupfile); hasGroup = true; }
sfftxtFilename = validParameter.valid(parameters, "sfftxt");
if (sfftxtFilename == "not found") { sfftxt = false; sfftxtFilename = ""; }
else if (util.isTrue(sfftxtFilename)) { sfftxt = true; sfftxtFilename = ""; }
else {
//you are a filename
if (inputDir != "") {
map<string,string>::iterator it = parameters.find("sfftxt");
//user has given a template file
if(it != parameters.end()){
string path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["sfftxt"] = inputDir + it->second; }
}
}
sfftxtFilename = validParameter.validFile(parameters, "sfftxt");
if (sfftxtFilename == "not found") { sfftxtFilename = ""; }
else if (sfftxtFilename == "not open") { sfftxtFilename = ""; abort = true; }
}
if ((hasGroup) || (hasOligos)) { split = 2; }
if (hasGroup && hasOligos) { m->mothurOut("[ERROR]: You may enter ONLY ONE of the following: oligos or group.\n"); abort = true; }
string temp = validParameter.valid(parameters, "qfile"); if (temp == "not found"){ temp = "T"; }
qual = util.isTrue(temp);
temp = validParameter.valid(parameters, "fasta"); if (temp == "not found"){ temp = "T"; }
fasta = util.isTrue(temp);
temp = validParameter.valid(parameters, "flow"); if (temp == "not found"){ temp = "T"; }
flow = util.isTrue(temp);
temp = validParameter.valid(parameters, "trim"); if (temp == "not found"){ temp = "T"; }
trim = util.isTrue(temp);
temp = validParameter.valid(parameters, "bdiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, bdiffs);
temp = validParameter.valid(parameters, "pdiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, pdiffs);
temp = validParameter.valid(parameters, "ldiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, ldiffs);
temp = validParameter.valid(parameters, "sdiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, sdiffs);
temp = validParameter.valid(parameters, "tdiffs"); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
util.mothurConvert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
temp = validParameter.valid(parameters, "checkorient"); if (temp == "not found") { temp = "F"; }
reorient = util.isTrue(temp);
}
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
exit(1);
}
}
//********************************************************************************
int SffInfoCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
long start = time(nullptr);
sffFilename = util.getFullPathName(sffFilename);
m->mothurOut("Extracting info from " + sffFilename + " ...\n" );
string oligos = "";
if (hasOligos) { oligos = oligosfile; }
if (hasGroup) { oligos = groupfile; }
int numReads = extractSffInfo(sffFilename, accnosName, oligos);
m->mothurOut("It took " + toString(time(nullptr) - start) + " secs to extract " + toString(numReads) + ".\n");
if (sfftxtFilename != "") { parseSffTxt(); }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setQualFile(currentName); }
}
itTypes = outputTypes.find("flow");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFlowFile(currentName); }
}
//report output filenames
m->mothurOut("\nOutput File Names:\n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]+"\n"); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "execute");
exit(1);
}
}
//**********************************************************************************
int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
try {
oligosObject = new Oligos();
currentFileName = input;
if (outputdir == "") { outputdir += util.hasPath(input); }
if (accnos != "") { seqNames.clear(); seqNames = util.readAccnos(accnos); }
else { seqNames.clear(); }
TrimOligos* trimOligos = nullptr; TrimOligos* rtrimOligos = nullptr;
if (hasOligos) {
readOligos(oligos); split = 2;
if (m->getControl_pressed()) { delete oligosObject; return 0; }
trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, oligosObject->getPrimers(), oligosObject->getBarcodes(), oligosObject->getReversePrimers(), oligosObject->getLinkers(), oligosObject->getSpacers()); numFPrimers = oligosObject->getPrimers().size(); numBarcodes = oligosObject->getBarcodes().size();
if (reorient) {
rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligosObject->getReorientedPairedPrimers(), oligosObject->getReorientedPairedBarcodes(), false); numBarcodes = oligosObject->getReorientedPairedBarcodes().size();
}
}
if (hasGroup) { readGroup(oligos); split = 2; }
ofstream outSfftxt, outFasta, outQual, outFlow;
string outFastaFileName, outQualFileName;
string rootName = outputdir + util.getRootName(util.getSimpleName(input));
if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
map<string, string> variables;
variables["[filename]"] = rootName;
string sfftxtFileName = getOutputFileName("sfftxt",variables);
string outFlowFileName = getOutputFileName("flow",variables);
if (!trim) { variables["[tag]"] = "raw"; }
outFastaFileName = getOutputFileName("fasta",variables);
outQualFileName = getOutputFileName("qfile",variables);
if (sfftxt) { util.openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); outputTypes["sfftxt"].push_back(sfftxtFileName); }
if (fasta) { util.openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
if (qual) { util.openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
if (flow) { util.openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName); }
ifstream in;
util.openInputFileBinary(input, in);
SffCommonHeader* header = new SffCommonHeader();
bool goodHeader = header->read(in);
if (!goodHeader) { delete oligosObject; if (hasOligos) { delete trimOligos; if (reorient) { delete rtrimOligos; } } return 0; }
//print common header
if (sfftxt) { header->printSFFTxt(outSfftxt); }
if (flow) { outFlow << header->getNumFlows() << endl; }
//read through the sff file
int count = 0; int numFlows = header->getNumFlows();
while (!in.eof()) {
bool print = true;
SffRead* read = new SffRead(in, numFlows);
if (!read->isOkay()) { break; }
if (split > 1) { assignToSample(read, trimOligos, rtrimOligos); }
//if you have provided an accosfile and this seq is not in it, then dont print
if (seqNames.size() != 0) { if (seqNames.count(read->getName()) == 0) { print = false; } }
//print
if (print) {
if (sfftxt) { read->printSffTxt(outSfftxt); }
if (fasta) { read->printFasta(outFasta, trim); }
if (qual) { read->printQuality(outQual, trim); }
if (flow) { read->printFlow(outFlow); }
}
count++;
delete read;
//report progress
if((count+1) % 10000 == 0){ m->mothurOutJustToScreen(toString(count+1)+"\n"); }
if (m->getControl_pressed()) { count = 0; break; }
if (count >= header->getNumReads()) { break; }
//if (count >= 10000) { break; } //debug
}
//report progress
if (!m->getControl_pressed()) { if((count) % 10000 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); } }
in.close();
if (sfftxt) { outSfftxt.close(); }
if (fasta) { outFasta.close(); }
if (qual) { outQual.close(); }
if (flow) { outFlow.close(); }
if (split > 1) {
//create new common headers for each file with the correct number of reads
adjustCommonHeader(header);
if (hasGroup) { delete groupMap; }
map<string, string>::iterator it;
set<string> namesToRemove;
for(int i=0;i<filehandles.size();i++){
for(int j=0;j<filehandles[0].size();j++){
if (filehandles[i][j] != "") {
if (namesToRemove.count(filehandles[i][j]) == 0) {
if (numSplitReads[i][j] == 0) {
util.mothurRemove(filehandles[i][j]);
util.mothurRemove(filehandlesHeaders[i][j]);
namesToRemove.insert(filehandles[i][j]);
}else {
if(util.isBlank(filehandles[i][j])){
util.mothurRemove(filehandles[i][j]);
util.mothurRemove(filehandlesHeaders[i][j]);
namesToRemove.insert(filehandles[i][j]);
}
}
}
}
}
}
//append new header to reads
for (int i = 0; i < filehandles.size(); i++) {
for (int j = 0; j < filehandles[i].size(); j++) {
if (filehandles[i][j] != "") {
if (namesToRemove.count(filehandles[i][j]) == 0) {
util.appendSFFFiles(filehandles[i][j], filehandlesHeaders[i][j]);
util.renameFile(filehandlesHeaders[i][j], filehandles[i][j]);
util.mothurRemove(filehandlesHeaders[i][j]);
}
}
}
}
//remove names for outputFileNames, just cleans up the output
for(int i = 0; i < outputNames.size(); i++) {
if (namesToRemove.count(outputNames[i]) != 0) {
outputNames.erase(outputNames.begin()+i);
i--;
}else { outputTypes["sff"].push_back(outputNames[i]); }
}
if(util.isBlank(noMatchFile)){ util.mothurRemove(noMatchFile); }
else { outputNames.push_back(noMatchFile); outputTypes["sff"].push_back(noMatchFile); }
}
delete header;
delete oligosObject;
if (hasOligos) { delete trimOligos; if (reorient) { delete rtrimOligos; } }
return count;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "extractSffInfo");
exit(1);
}
}
//****************************************************************************************
int SffInfoCommand::adjustCommonHeader(SffCommonHeader*& header){
try {
string endian = util.findEdianness();
for (int i = 0; i < filehandlesHeaders.size(); i++) {
for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
ofstream out; util.openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
header->printSampleCommonHeader(out, numSplitReads[i][j]);
out.close();
}
}
ofstream outNoMatchHeader;
string tempNoHeader = "tempNoMatchHeader";
util.openOutputFileBinary(tempNoHeader, outNoMatchHeader);
header->printSampleCommonHeader(outNoMatchHeader, numNoMatch); outNoMatchHeader.close();
util.appendSFFFiles(noMatchFile, tempNoHeader);
util.renameFile(tempNoHeader, noMatchFile);
util.mothurRemove(tempNoHeader);
return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "adjustCommonHeader");
exit(1);
}
}
//***********************************************************************************************
void SffInfoCommand::assignToSample(SffRead*& read, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos){
try {
int barcodeIndex, primerIndex, trashCodeLength; trashCodeLength = 0; primerIndex = 0; barcodeIndex = 0;
if (hasOligos) { trashCodeLength = findGroup(read, barcodeIndex, primerIndex, trimOligos, rtrimOligos); }
else if (hasGroup) { trashCodeLength = findGroup(read, barcodeIndex, primerIndex, "groupMode"); }
else { m->mothurOut("[ERROR]: uh oh, we shouldn't be here...\n"); }
if(trashCodeLength == 0){
ofstream out; util.openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
read->printSff(out); out.close();
numSplitReads[barcodeIndex][primerIndex]++;
}
else{
ofstream out; util.openOutputFileBinaryAppend(noMatchFile, out);
read->printSff(out); out.close();
numNoMatch++;
}
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "assignToSample");
exit(1);
}
}
//***************************************************************************************************
int SffInfoCommand::findGroup(SffRead*& read, int& barcode, int& primer, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos) {
try {
int success = 1;
string trashCode = "";
int currentSeqsDiffs = 0;
string seq = read->getBases();
int readLength = read->getBases().length();
unsigned short clipLeft = read->getClipQualLeft();
unsigned short clipRight = read->getClipQualRight();
for (int i = 0; i < readLength; i++) { seq[i] = toupper(seq[i]); }
if (trim) {
if(clipRight < clipLeft){
//don't trim right
if (clipRight == 0) { seq = seq.substr(clipLeft-1); }
else { seq = "NNNN"; }
}
else if((clipRight != 0) && ((clipRight-clipLeft) >= 0)){ seq = seq.substr((clipLeft-1), (clipRight-clipLeft+1)); }
else { seq = seq.substr(clipLeft-1); }
}
Sequence currSeq(read->getName(), seq);
Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
if(numLinkers != 0){
success = trimOligos->stripLinker(currSeq);
if(success > ldiffs) { trashCode += 'k'; }
else{ currentSeqsDiffs += success; }
}
if(numBarcodes != 0){
vector<int> results = trimOligos->stripBarcode(currSeq, barcode);
if (pairedOligos) { success = results[0] + results[2]; }
else { success = results[0]; }
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(numSpacers != 0){
success = trimOligos->stripSpacer(currSeq);
if(success > sdiffs) { trashCode += 's'; }
else{ currentSeqsDiffs += success; }
}
if(numFPrimers != 0){
vector<int> results = trimOligos->stripForward(currSeq, primer);
if (pairedOligos) { success = results[0] + results[2]; }
else { success = results[0]; }
if(success > pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
if(numRPrimers != 0){
vector<int> results = trimOligos->stripReverse(currSeq);
success = results[0];
if(success > pdiffs) { trashCode += 'r'; }
else{ currentSeqsDiffs += success; }
}
if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
int thisSuccess = 0;
string thisTrashCode = "";
int thisCurrentSeqsDiffs = 0;
int thisBarcodeIndex = 0;
int thisPrimerIndex = 0;
if(numBarcodes != 0){
vector<int> results = rtrimOligos->stripBarcode(savedSeq, thisBarcodeIndex);
if (pairedOligos) { thisSuccess = results[0] + results[2]; }
else { thisSuccess = results[0]; }
if(thisSuccess > bdiffs) { thisTrashCode += "b"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if(numFPrimers != 0){
vector<int> results = rtrimOligos->stripForward(savedSeq, thisPrimerIndex);
if (pairedOligos) { thisSuccess = results[0] + results[2]; }
else { thisSuccess = results[0]; }
if(thisSuccess > pdiffs) { thisTrashCode += "f"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
if (thisTrashCode == "") {
trashCode = thisTrashCode;
success = thisSuccess;
currentSeqsDiffs = thisCurrentSeqsDiffs;
barcode = thisBarcodeIndex;
primer = thisPrimerIndex;
}else { trashCode += "(" + thisTrashCode + ")"; }
}
if (trashCode.length() == 0) { //is this sequence in the ignore group
string thisGroup = oligosObject->getGroupName(barcode, primer);
int pos = thisGroup.find("ignore");
if (pos != string::npos) { trashCode += "i"; }
}
return trashCode.length();
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "findGroup");
exit(1);
}
}
//***************************************************************************************
int SffInfoCommand::findGroup(SffRead*& read, int& barcode, int& primer, string groupMode) {
try {
string trashCode = "";
primer = 0;
string group = groupMap->getGroup(read->getName());
if (group == "not found") { trashCode += "g"; } //scrap for group
else { barcode = GroupToFile[group]; }
return trashCode.length();
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "findGroup");
exit(1);
}
}
//***********************************************************************************
int SffInfoCommand::parseSffTxt() {
try {
ifstream inSFF;
util.openInputFile(sfftxtFilename, inSFF);
if (outputdir == "") { outputdir += util.hasPath(sfftxtFilename); }
//output file names
ofstream outFasta, outQual, outFlow;
string outFastaFileName, outQualFileName;
string fileRoot = util.getRootName(util.getSimpleName(sfftxtFilename));
if (fileRoot.length() > 0) {
//rip off last .
fileRoot = fileRoot.substr(0, fileRoot.length()-1);
fileRoot = util.getRootName(fileRoot);
}
map<string, string> variables;
variables["[filename]"] = fileRoot;
string sfftxtFileName = getOutputFileName("sfftxt",variables);
string outFlowFileName = getOutputFileName("flow",variables);
if (!trim) { variables["[tag]"] = "raw"; }
outFastaFileName = getOutputFileName("fasta",variables);
outQualFileName = getOutputFileName("qfile",variables);
if (fasta) { util.openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
if (qual) { util.openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
if (flow) { util.openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName); }
//read common header
string commonHeader = util.getline(inSFF);
string magicNumber = util.getline(inSFF);
string version = util.getline(inSFF);
string indexOffset = util.getline(inSFF);
string indexLength = util.getline(inSFF);
int numReads = parseHeaderLineToInt(inSFF);
string headerLength = util.getline(inSFF);
string keyLength = util.getline(inSFF);
int numFlows = parseHeaderLineToInt(inSFF);
string flowgramCode = util.getline(inSFF);
string flowChars = util.getline(inSFF);
string keySequence = util.getline(inSFF);
gobble(inSFF);
string seqName;
if (flow) { outFlow << numFlows << endl; }
for(int i=0;i<numReads;i++){
//sanity check
if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + ".\n"); break; }
SffRead read(numFlows);
//parse read header
inSFF >> seqName;
seqName = seqName.substr(1);
gobble(inSFF);
read.setName(seqName);
string runPrefix = parseHeaderLineToString(inSFF); read.setTimeStamp(runPrefix);
string regionNumber = parseHeaderLineToString(inSFF); read.setRegion(regionNumber);
string xyLocation = parseHeaderLineToString(inSFF); read.setXY(xyLocation);
gobble(inSFF);
string runName = parseHeaderLineToString(inSFF);
string analysisName = parseHeaderLineToString(inSFF);
string fullPath = parseHeaderLineToString(inSFF);
gobble(inSFF);
unsigned short readHeaderLen = parseHeaderLineToShort(inSFF); read.setHeaderLength(readHeaderLen);
unsigned short nameLength = parseHeaderLineToShort(inSFF); read.setNameLength(nameLength);
int numBases = parseHeaderLineToInt(inSFF); read.setNumBases(numBases);
unsigned short clipQualLeft = parseHeaderLineToShort(inSFF); read.setClipQualLeft(clipQualLeft);
unsigned short clipQualRight = parseHeaderLineToShort(inSFF); read.setClipQualRight(clipQualRight);
unsigned short clipAdapLeft = parseHeaderLineToShort(inSFF); read.setClipAdapterLeft(clipAdapLeft);
unsigned short clipAdapRight = parseHeaderLineToShort(inSFF); read.setClipAdapterRight(clipAdapRight);
gobble(inSFF);
//parse read
vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows); read.setFlowgrams(flowVector);
vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
//adjust for print
vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
for (int j = 1; j < flowIndices.size(); j++) { flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]); }
read.setFlowIndex(flowIndicesAdjusted);
string bases = parseHeaderLineToString(inSFF); read.setBases(bases);
vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases); read.setQualScores(qualityScores);
gobble(inSFF);
//if you have provided an accosfile and this seq is not in it, then dont print
bool print = true;
if (seqNames.size() != 0) { if (seqNames.count(read.getName()) == 0) { print = false; } }
//print
if (print) {
if (fasta) { read.printFasta(outFasta, trim); }
if (qual) { read.printQuality(outQual, trim); }
if (flow) { read.printFlow(outFlow); }
}
//report progress
if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)+"\n"); }
if (m->getControl_pressed()) { break; }
}
//report progress
if (!m->getControl_pressed()) { if((numReads) % 10000 != 0){ m->mothurOut(toString(numReads)+"\n"); } }
inSFF.close();
if (fasta) { outFasta.close(); }
if (qual) { outQual.close(); }
if (flow) { outFlow.close(); }
return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "parseSffTxt");
exit(1);
}
}
//*****************************************************************************
int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
try {
int number = 0;
while (!file.eof()) {
char c = file.get();
if (c == ':'){ file >> number; break; }
}
gobble(file);
return number;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
exit(1);
}
}
//*****************************************************************************
unsigned short SffInfoCommand::parseHeaderLineToShort(ifstream& file){
try {
string text;
while (!file.eof()) {
char c = file.get();
if (c == ':'){ file >> text; break; }
}
gobble(file);
unsigned short value;
util.mothurConvert(text, value);
return value;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "parseHeaderLineToShort");
exit(1);
}
}
//*****************************************************************************
string SffInfoCommand::parseHeaderLineToString(ifstream& file){
try {
string text;
while (!file.eof()) {
char c = file.get();
if (c == ':'){ file >> text; break; }
}
gobble(file);
return text;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
exit(1);
}
}
//********************************************************************************************
vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
try {
vector<unsigned short> floatVector(length);
while (!file.eof()) {
char c = file.get();
if (c == ':'){
float temp;
for(int i=0;i<length;i++){ file >> temp; floatVector[i] = temp * 100; }
break;
}
}
gobble(file);
return floatVector;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
exit(1);
}
}
//******************************************************************************************
vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
try {
vector<unsigned int> intVector(length);
while (!file.eof()) {
char c = file.get();
if (c == ':'){
for(int i=0;i<length;i++){ file >> intVector[i]; }
break;
}
}
gobble(file);
return intVector;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
exit(1);
}
}
//***********************************************************************************************
bool SffInfoCommand::readOligos(string oligoFile){
try {
filehandles.clear();
numSplitReads.clear();
filehandlesHeaders.clear();
bool allBlank = false;
oligosObject->read(oligoFile);
if (m->getControl_pressed()) { return false; } //error in reading oligos
if (oligosObject->hasPairedPrimers() || oligosObject->hasPairedBarcodes()) {
pairedOligos = true;
m->mothurOut("[ERROR]: sffinfo does not support paired barcodes and primers, aborting.\n"); m->setControl_pressed(true); return true;
}else {
pairedOligos = false;
numFPrimers = oligosObject->getPrimers().size();
numBarcodes = oligosObject->getBarcodes().size();
}
numLinkers = oligosObject->getLinkers().size();
numSpacers = oligosObject->getSpacers().size();
numRPrimers = oligosObject->getReversePrimers().size();
vector<string> groupNames = oligosObject->getGroupNames();
if (groupNames.size() == 0) { allBlank = true; }
filehandles.resize(oligosObject->getBarcodeNames().size());
for(int i=0;i<filehandles.size();i++){
for(int j=0;j<oligosObject->getPrimerNames().size();j++){ filehandles[i].push_back(""); }
}
if(split > 1){
set<string> uniqueNames; //used to cleanup outputFileNames
map<string, int> barcodes = oligosObject->getBarcodes() ;
map<string, int> primers = oligosObject->getPrimers();
for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
string primerName = oligosObject->getPrimerName(itPrimer->second);
string barcodeName = oligosObject->getBarcodeName(itBar->second);
if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
else if ((primerName == "") && (barcodeName == "")) { } //do nothing
else {
string comboGroupName = "";
string comboName = "";
if(primerName == ""){
comboGroupName = barcodeName;
}else{
if(barcodeName == ""){
comboGroupName = primerName;
}
else{
comboGroupName = barcodeName + "." + primerName;
}
}
if(itPrimer->first == ""){
comboName = itBar->first;
}else{
if(itBar->first == ""){
comboName = itPrimer->first;
}
else{
comboName = itBar->first + "." + itPrimer->first;
}
}
if (comboName != "") { comboGroupName += "_" + comboName; }
ofstream temp;
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(currentFileName));
variables["[group]"] = comboGroupName;
string thisFilename = getOutputFileName("sff",variables);
if (uniqueNames.count(thisFilename) == 0) {
outputNames.push_back(thisFilename);
uniqueNames.insert(thisFilename);
}
filehandles[itBar->second][itPrimer->second] = thisFilename;
util.openOutputFileBinary(thisFilename, temp); temp.close();
}
}
}
}
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(currentFileName));
variables["[group]"] = "scrap";
noMatchFile = getOutputFileName("sff",variables);
util.mothurRemove(noMatchFile);
numNoMatch = 0;
filehandlesHeaders.resize(filehandles.size());
numSplitReads.resize(filehandles.size());
for (int i = 0; i < filehandles.size(); i++) {
numSplitReads[i].resize(filehandles[i].size(), 0);
for (int j = 0; j < filehandles[i].size(); j++) {
filehandlesHeaders[i].push_back(filehandles[i][j]+"headers");
ofstream temp;
util.openOutputFileBinary(filehandles[i][j]+"headers", temp); temp.close();
}
}
if (allBlank) {
m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a split the sff file.\n");
split = 1;
return false;
}
return true;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readOligos");
exit(1);
}
}
//***************************************************************************************************
bool SffInfoCommand::readGroup(string oligoFile){
try {
filehandles.clear();
numSplitReads.clear();
filehandlesHeaders.clear();
groupMap = new GroupMap();
groupMap->readMap(oligoFile);
//like barcodeNameVector - no primer names
vector<string> groups = groupMap->getNamesOfGroups();
filehandles.resize(groups.size());
for (int i = 0; i < filehandles.size(); i++) {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(currentFileName));
variables["[group]"] = groups[i];
string thisFilename = getOutputFileName("sff",variables);
outputNames.push_back(thisFilename);
ofstream temp;
util.openOutputFileBinary(thisFilename, temp); temp.close();
filehandles[i].push_back(thisFilename);
GroupToFile[groups[i]] = i;
}
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(currentFileName));
variables["[group]"] = "scrap";
noMatchFile = getOutputFileName("sff",variables);
util.mothurRemove(noMatchFile);
numNoMatch = 0;
filehandlesHeaders.resize(groups.size());
numSplitReads.resize(filehandles.size());
for (int i = 0; i < filehandles.size(); i++) {
numSplitReads[i].resize(filehandles[i].size(), 0);
for (int j = 0; j < filehandles[i].size(); j++) {
string thisHeader = filehandles[i][j]+"headers";
filehandlesHeaders[i].push_back(thisHeader);
ofstream temp;
util.openOutputFileBinary(thisHeader, temp); temp.close();
}
}
return true;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readGroup");
exit(1);
}
}
//********************************************************************/
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