#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", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+ 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 pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ 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 sfftxt file.\n";
+ helpString += "The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, oligos, bdiffs, tdiffs, ldiffs, sdiffs, pdiffs and trim. sff is required. \n";
+ helpString += "The sff parameter allows you to enter the sff file you would like to extract data from. You may enter multiple files by separating them by -'s.\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 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 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. You may enter multiple files by separating them by -'s. \n";
+ helpString += "Example sffinfo(sff=mySffFile.sff, trim=F).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\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->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SffInfoCommand::SffInfoCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
+ outputTypes["sfftxt"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ outputTypes["sff"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SffInfoCommand::SffInfoCommand(string option) {
try {
- abort = false;
- hasAccnos = false;
+ abort = false; calledHelp = false;
+ hasAccnos = false; hasOligos = false;
+ split = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
//valid paramters for this command
- string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
+ outputTypes["sfftxt"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ outputTypes["sff"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; }
sffFilename = validParameter.validFile(parameters, "sff", false);
- if (sffFilename == "not found") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true; }
+ if (sffFilename == "not found") { sffFilename = ""; }
else {
- splitAtDash(sffFilename, filenames);
+ m->splitAtDash(sffFilename, filenames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < filenames.size(); i++) {
- if (inputDir != "") {
- string path = hasPath(filenames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { filenames[i] = inputDir + filenames[i]; }
- }
-
- ifstream in;
- int ableToOpen = openInputFile(filenames[i], in, "noerror");
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(filenames[i]);
- m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
- filenames[i] = tryPath;
+ bool ignore = false;
+ if (filenames[i] == "current") {
+ filenames[i] = m->getSFFFile();
+ if (filenames[i] != "") { m->mothurOut("Using " + filenames[i] + " as input file for the sff parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current sfffile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ filenames.erase(filenames.begin()+i);
+ i--;
}
}
- in.close();
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- filenames.erase(filenames.begin()+i);
- i--;
+ if (!ignore) {
+ if (inputDir != "") {
+ string path = m->hasPath(filenames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { filenames[i] = inputDir + filenames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
+ m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ filenames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
+ m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ filenames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ filenames.erase(filenames.begin()+i);
+ i--;
+ }else { m->setSFFFile(filenames[i]); }
}
}
if (accnosName == "not found") { accnosName = ""; }
else {
hasAccnos = true;
- splitAtDash(accnosName, accnosFileNames);
+ m->splitAtDash(accnosName, accnosFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < accnosFileNames.size(); i++) {
- if (inputDir != "") {
- string path = hasPath(accnosFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { accnosFileNames[i] = inputDir + accnosFileNames[i]; }
+ bool ignore = false;
+ if (accnosFileNames[i] == "current") {
+ accnosFileNames[i] = m->getAccnosFile();
+ if (accnosFileNames[i] != "") { m->mothurOut("Using " + accnosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current accnosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ accnosFileNames.erase(accnosFileNames.begin()+i);
+ i--;
+ }
}
-
- ifstream in;
- int ableToOpen = openInputFile(accnosFileNames[i], in, "noerror");
+
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(accnosFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { accnosFileNames[i] = inputDir + accnosFileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ accnosFileNames[i] = tryPath;
+ }
+ }
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ accnosFileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ accnosFileNames.erase(accnosFileNames.begin()+i);
+ i--;
+ }
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ oligosfile = validParameter.validFile(parameters, "oligos", false);
+ if (oligosfile == "not found") { oligosfile = ""; }
+ else {
+ hasOligos = true;
+ m->splitAtDash(oligosfile, oligosFileNames);
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(accnosFileNames[i]);
- m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
- accnosFileNames[i] = tryPath;
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < oligosFileNames.size(); i++) {
+ bool ignore = false;
+ if (oligosFileNames[i] == "current") {
+ oligosFileNames[i] = m->getOligosFile();
+ if (oligosFileNames[i] != "") { m->mothurOut("Using " + oligosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current oligosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ oligosFileNames.erase(oligosFileNames.begin()+i);
+ i--;
}
}
- in.close();
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- accnosFileNames.erase(accnosFileNames.begin()+i);
- i--;
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(oligosFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { oligosFileNames[i] = inputDir + oligosFileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(oligosFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(oligosFileNames[i]);
+ m->mothurOut("Unable to open " + oligosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ oligosFileNames[i] = tryPath;
+ }
+ }
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(oligosFileNames[i]);
+ m->mothurOut("Unable to open " + oligosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ oligosFileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + oligosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ oligosFileNames.erase(oligosFileNames.begin()+i);
+ i--;
+ }
}
}
//make sure there is at least one valid file left
- if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ if (oligosFileNames.size() == 0) { m->mothurOut("no valid oligos files."); m->mothurOutEndLine(); abort = true; }
}
-
+
+ if (hasOligos) {
+ split = 2;
+ if (oligosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a oligos file, you must have one for each sff file."); m->mothurOutEndLine(); }
+ }
+
if (hasAccnos) {
if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }
}
string temp = validParameter.validFile(parameters, "qfile", false); if (temp == "not found"){ temp = "T"; }
- qual = isTrue(temp);
+ qual = m->isTrue(temp);
temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; }
- fasta = isTrue(temp);
+ fasta = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; }
- flow = isTrue(temp);
+ temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "T"; }
+ flow = m->isTrue(temp);
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
- trim = isTrue(temp);
+ trim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
- temp = validParameter.validFile(parameters, "sfftxt", false); if (temp == "not found"){ temp = "F"; }
- sfftxt = isTrue(temp);
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
+
+ temp = validParameter.validFile(parameters, "sfftxt", false);
+ if (temp == "not found") { temp = "F"; sfftxt = false; sfftxtFilename = ""; }
+ else if (m->isTrue(temp)) { 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 = m->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", true);
+ if (sfftxtFilename == "not found") { sfftxtFilename = ""; }
+ else if (sfftxtFilename == "not open") { sfftxtFilename = ""; }
+ }
+
+ if ((sfftxtFilename == "") && (filenames.size() == 0)) {
+ //if there is a current sff file, use it
+ string filename = m->getSFFFile();
+ if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true; }
+ }
+
+
}
}
catch(exception& e) {
exit(1);
}
}
-//**********************************************************************************************************************
-
-void SffInfoCommand::help(){
- try {
- m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data.\n");
- m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");
- m->mothurOut("The sff parameter allows you to enter the sff file you would like to extract data from. You may enter multiple files by separating them by -'s.\n");
- m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated. Default=True. \n");
- m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated. Default=True. \n");
- m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated. Default=False. \n");
- m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. Default=False. \n");
- m->mothurOut("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");
- m->mothurOut("The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n");
- m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-SffInfoCommand::~SffInfoCommand(){}
-
//**********************************************************************************************************************
int SffInfoCommand::execute(){
try {
-
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < filenames.size(); s++) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
int start = time(NULL);
+ filenames[s] = m->getFullPathName(filenames[s]);
m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
string accnos = "";
if (hasAccnos) { accnos = accnosFileNames[s]; }
+
+ string oligos = "";
+ if (hasOligos) { oligos = oligosFileNames[s]; }
- int numReads = extractSffInfo(filenames[s], accnos);
+ int numReads = extractSffInfo(filenames[s], accnos, oligos);
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (sfftxtFilename != "") { parseSffTxt(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("qfile");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+ }
+
+ itTypes = outputTypes.find("flow");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
+ }
//report output filenames
m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
-int SffInfoCommand::extractSffInfo(string input, string accnos){
+int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
try {
-
- if (outputDir == "") { outputDir += hasPath(input); }
+ currentFileName = input;
+ if (outputDir == "") { outputDir += m->hasPath(input); }
if (accnos != "") { readAccnosFile(accnos); }
else { seqNames.clear(); }
+
+ if (oligos != "") { readOligos(oligos); split = 2; }
ofstream outSfftxt, outFasta, outQual, outFlow;
string outFastaFileName, outQualFileName;
- string sfftxtFileName = outputDir + getRootName(getSimpleName(input)) + "sff.txt";
- string outFlowFileName = outputDir + getRootName(getSimpleName(input)) + "flow";
- if (trim) {
- outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "fasta";
- outQualFileName = outputDir + getRootName(getSimpleName(input)) + "qual";
- }else{
- outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "raw.fasta";
- outQualFileName = outputDir + getRootName(getSimpleName(input)) + "raw.qual";
- }
-
- if (sfftxt) { openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); }
- if (fasta) { openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); }
- if (qual) { openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); }
- if (flow) { openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); }
+ string rootName = outputDir + m->getRootName(m->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) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); outputTypes["sfftxt"].push_back(sfftxtFileName); }
+ if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
+ if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
+ if (flow) { m->openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName); }
ifstream in;
in.open(input.c_str(), ios::binary);
CommonHeader header;
readCommonHeader(in, header);
-
+
int count = 0;
+ mycount = 0;
//check magic number and version
if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
//print common header
- if (sfftxt) { printCommonHeader(outSfftxt, header); }
-
+ if (sfftxt) { printCommonHeader(outSfftxt, header); }
+ if (flow) { outFlow << header.numFlowsPerRead << endl; }
+
//read through the sff file
while (!in.eof()) {
bool print = true;
-
- //read header
- Header readheader;
- readHeader(in, readheader);
-
+
//read data
- seqRead read;
- readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
-
+ seqRead read; Header readheader;
+ readSeqData(in, read, header.numFlowsPerRead, readheader);
+ bool okay = sanityCheck(readheader, read);
+ if (!okay) { break; }
+
//if you have provided an accosfile and this seq is not in it, then dont print
if (seqNames.size() != 0) { if (seqNames.count(readheader.name) == 0) { print = false; } }
}
count++;
-
+ mycount++;
+
//report progress
if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
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);
+
+ 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(m->isBlank(filehandles[i][j])){
+ m->mothurRemove(filehandles[i][j]);
+ m->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++) {
+ m->appendFiles(filehandles[i][j], filehandlesHeaders[i][j]);
+ m->renameFile(filehandlesHeaders[i][j], filehandles[i][j]);
+ m->mothurRemove(filehandlesHeaders[i][j]);
+ if (numSplitReads[i][j] == 0) { m->mothurRemove(filehandles[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--;
+ }
+ }
+
+ if(m->isBlank(noMatchFile)){ m->mothurRemove(noMatchFile); }
+ else { outputNames.push_back(noMatchFile); outputTypes["sff"].push_back(noMatchFile); }
+ }
+
return count;
}
catch(exception& e) {
//**********************************************************************************************************************
int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
try {
-
+
if (!in.eof()) {
//read magic number
char buffer[4];
in.read(buffer, 4);
header.magicNumber = be_int4(*(unsigned int *)(&buffer));
-
+
//read version
char buffer9[4];
in.read(buffer9, 4);
header.version = "";
- for (int i = 0; i < 4; i++) { header.version += toString((int)(buffer9[i])); }
-
+ for (int i = 0; i < 4; i++) { header.version += toString((int)(buffer9[i])); }
+
//read offset
char buffer2 [8];
in.read(buffer2, 8);
- header.indexOffset = be_int8(*(unsigned long int *)(&buffer2));
+ header.indexOffset = be_int8(*(unsigned long long *)(&buffer2));
//read index length
char buffer3 [4];
in.read(buffer3, 4);
header.indexLength = be_int4(*(unsigned int *)(&buffer3));
-
+
//read num reads
char buffer4 [4];
in.read(buffer4, 4);
header.keySequence = tempBuffer2;
if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength); }
delete[] tempBuffer2;
-
+
/* Pad to 8 chars */
- unsigned long int spotInFile = in.tellg();
- unsigned long int spot = (spotInFile + 7)& ~7; // ~ inverts
+ unsigned long long spotInFile = in.tellg();
+ unsigned long long spot = (spotInFile + 7)& ~7; // ~ inverts
in.seekg(spot);
-
- }else{
+
+ }else{
m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
}
-
+
return 0;
+
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readCommonHeader");
}
}
//**********************************************************************************************************************
-int SffInfoCommand::readHeader(ifstream& in, Header& header){
+int SffInfoCommand::adjustCommonHeader(CommonHeader header){
try {
-
- if (!in.eof()) {
+
+ char* mybuffer = new char[4];
+ ifstream in;
+ in.open(currentFileName.c_str(), ios::binary);
+
+ //magic number
+ in.read(mybuffer,4);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //version
+ mybuffer = new char[4];
+ in.read(mybuffer,4);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //offset
+ mybuffer = new char[8];
+ in.read(mybuffer,8);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ unsigned long long offset = 0;
+ char* thisbuffer = new char[8];
+ thisbuffer[0] = (offset >> 56) & 0xFF;
+ thisbuffer[1] = (offset >> 48) & 0xFF;
+ thisbuffer[2] = (offset >> 40) & 0xFF;
+ thisbuffer[3] = (offset >> 32) & 0xFF;
+ thisbuffer[4] = (offset >> 24) & 0xFF;
+ thisbuffer[5] = (offset >> 16) & 0xFF;
+ thisbuffer[6] = (offset >> 8) & 0xFF;
+ thisbuffer[7] = offset & 0xFF;
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(thisbuffer, 8);
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
- //read header length
+ //read index length
+ mybuffer = new char[4];
+ in.read(mybuffer,4);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ int offset = 0;
+ char* thisbuffer = new char[4];
+ thisbuffer[0] = (offset >> 24) & 0xFF;
+ thisbuffer[1] = (offset >> 16) & 0xFF;
+ thisbuffer[2] = (offset >> 8) & 0xFF;
+ thisbuffer[3] = offset & 0xFF;
+ out.write(thisbuffer, 4);
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //change num reads
+ mybuffer = new char[4];
+ in.read(mybuffer,4);
+ delete[] mybuffer;
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ //convert number of reads to 4 byte char*
+ char* thisbuffer = new char[4];
+ thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
+ thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
+ thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
+ thisbuffer[3] = numSplitReads[i][j] & 0xFF;
+ out.write(thisbuffer, 4);
+ out.close();
+ delete[] thisbuffer;
+ }
+ }
+
+ //read header length
+ mybuffer = new char[2];
+ in.read(mybuffer,2);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //read key length
+ mybuffer = new char[2];
+ in.read(mybuffer,2);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //read number of flow reads
+ mybuffer = new char[2];
+ in.read(mybuffer,2);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //read format code
+ mybuffer = new char[1];
+ in.read(mybuffer,1);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //read flow chars
+ mybuffer = new char[header.numFlowsPerRead];
+ in.read(mybuffer,header.numFlowsPerRead);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+ //read key
+ mybuffer = new char[header.keyLength];
+ in.read(mybuffer,header.keyLength);
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, in.gcount());
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+
+
+ /* Pad to 8 chars */
+ unsigned long long spotInFile = in.tellg();
+ unsigned long long spot = (spotInFile + 7)& ~7; // ~ inverts
+ in.seekg(spot);
+
+ mybuffer = new char[spot-spotInFile];
+ for (int i = 0; i < filehandlesHeaders.size(); i++) {
+ for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+ ofstream out;
+ m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
+ out.write(mybuffer, spot-spotInFile);
+ out.close();
+ }
+ }
+ delete[] mybuffer;
+ in.close();
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "adjustCommonHeader");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, Header& header){
+ try {
+ unsigned long long startSpotInFile = in.tellg();
+ if (!in.eof()) {
+
+ /*****************************************/
+ //read header
+
+ //read header length
char buffer [2];
in.read(buffer, 2);
header.headerLength = be_int2(*(unsigned short *)(&buffer));
-
+
//read name length
char buffer2 [2];
in.read(buffer2, 2);
header.nameLength = be_int2(*(unsigned short *)(&buffer2));
-
+
//read num bases
char buffer3 [4];
in.read(buffer3, 4);
char buffer4 [2];
in.read(buffer4, 2);
header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4));
+ header.clipQualLeft = 5;
//read clip qual right
char buffer5 [2];
in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
- if(header.clipQualRight == 0){ header.clipQualRight = header.numBases; }
-
+
//read clipAdapterLeft
char buffer6 [2];
in.read(buffer6, 2);
header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
-
+
//read clipAdapterRight
char buffer7 [2];
in.read(buffer7, 2);
header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
-
+
//read name
char* tempBuffer = new char[header.nameLength];
in.read(&(*tempBuffer), header.nameLength);
if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength); }
delete[] tempBuffer;
+ //extract info from name
+ decodeName(header.timestamp, header.region, header.xy, header.name);
+
/* Pad to 8 chars */
- unsigned long int spotInFile = in.tellg();
- unsigned long int spot = (spotInFile + 7)& ~7;
+ unsigned long long spotInFile = in.tellg();
+ unsigned long long spot = (spotInFile + 7)& ~7;
in.seekg(spot);
-
- }else{
- m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
- }
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "readHeader");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
- try {
-
- if (!in.eof()) {
-
+ /*****************************************/
+ //sequence read
+
//read flowgram
read.flowgram.resize(numFlowReads);
for (int i = 0; i < numFlowReads; i++) {
in.read(buffer, 2);
read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
}
-
+
//read flowIndex
- read.flowIndex.resize(numBases);
- for (int i = 0; i < numBases; i++) {
+ read.flowIndex.resize(header.numBases);
+ for (int i = 0; i < header.numBases; i++) {
char temp[1];
in.read(temp, 1);
read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
}
//read bases
- char* tempBuffer = new char[numBases];
- in.read(&(*tempBuffer), numBases);
- read.bases = tempBuffer;
- if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases); }
- delete[] tempBuffer;
+ char* tempBuffer6 = new char[header.numBases];
+ in.read(&(*tempBuffer6), header.numBases);
+ read.bases = tempBuffer6;
+ if (read.bases.length() > header.numBases) { read.bases = read.bases.substr(0, header.numBases); }
+ delete[] tempBuffer6;
//read qual scores
- read.qualScores.resize(numBases);
- for (int i = 0; i < numBases; i++) {
+ read.qualScores.resize(header.numBases);
+ for (int i = 0; i < header.numBases; i++) {
char temp[1];
in.read(temp, 1);
read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
}
/* Pad to 8 chars */
- unsigned long int spotInFile = in.tellg();
- unsigned long int spot = (spotInFile + 7)& ~7;
+ spotInFile = in.tellg();
+ spot = (spotInFile + 7)& ~7;
in.seekg(spot);
-
+
+ if (split > 1) {
+ char * mybuffer;
+ mybuffer = new char [spot-startSpotInFile];
+ ifstream in2;
+ in2.open(currentFileName.c_str(), ios::binary);
+ in2.seekg(startSpotInFile);
+ in2.read(mybuffer,spot-startSpotInFile);
+ in2.close();
+
+ int barcodeIndex, primerIndex;
+ int trashCodeLength = findGroup(header, read, barcodeIndex, primerIndex);
+
+ if(trashCodeLength == 0){
+ ofstream out;
+ m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
+ out.write(mybuffer, in2.gcount());
+ out.close();
+ delete[] mybuffer;
+ numSplitReads[barcodeIndex][primerIndex]++;
+ }
+ else{
+ ofstream out;
+ m->openOutputFileBinaryAppend(noMatchFile, out);
+ out.write(mybuffer, in2.gcount());
+ out.close();
+ delete[] mybuffer;
+ }
+
+ }
}else{
m->mothurOut("Error reading."); m->mothurOutEndLine();
}
}
}
//**********************************************************************************************************************
+int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& primer) {
+ try {
+ //find group read belongs to
+ TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
+
+ int success = 1;
+ string trashCode = "";
+ int currentSeqsDiffs = 0;
+
+ string seq = read.bases;
+
+ if (trim) {
+ if(header.clipQualRight < header.clipQualLeft){
+ if (header.clipQualRight == 0) { //don't trim right
+ seq = seq.substr(header.clipQualLeft-1);
+ }else {
+ seq = "NNNN";
+ }
+ }
+ else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
+ seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
+ }
+ else {
+ seq = seq.substr(header.clipQualLeft-1);
+ }
+ }else{
+ //if you wanted the sfftxt then you already converted the bases to the right case
+ if (!sfftxt) {
+ int endValue = header.clipQualRight;
+ //make the bases you want to clip lowercase and the bases you want to keep upper case
+ if(endValue == 0){ endValue = seq.length(); }
+ for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
+ }
+ }
+
+ Sequence currSeq(header.name, seq);
+ QualityScores currQual;
+
+ if(numLinkers != 0){
+ success = trimOligos.stripLinker(currSeq, currQual);
+ if(success > ldiffs) { trashCode += 'k'; }
+ else{ currentSeqsDiffs += success; }
+
+ }
+
+ if(barcodes.size() != 0){
+ success = trimOligos.stripBarcode(currSeq, currQual, barcode);
+ if(success > bdiffs) { trashCode += 'b'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if(numSpacers != 0){
+ success = trimOligos.stripSpacer(currSeq, currQual);
+ if(success > sdiffs) { trashCode += 's'; }
+ else{ currentSeqsDiffs += success; }
+
+ }
+
+ if(numFPrimers != 0){
+ success = trimOligos.stripForward(currSeq, currQual, primer, true);
+ if(success > pdiffs) { trashCode += 'f'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
+
+ if(revPrimer.size() != 0){
+ success = trimOligos.stripReverse(currSeq, currQual);
+ if(!success) { trashCode += 'r'; }
+ }
+
+
+ return trashCode.length();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "findGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
+ try {
+
+ if (name.length() >= 6) {
+ string time = name.substr(0, 6);
+ unsigned int timeNum = m->fromBase36(time);
+
+ int q1 = timeNum / 60;
+ int sec = timeNum - 60 * q1;
+ int q2 = q1 / 60;
+ int minute = q1 - 60 * q2;
+ int q3 = q2 / 24;
+ int hr = q2 - 24 * q3;
+ int q4 = q3 / 32;
+ int day = q3 - 32 * q4;
+ int q5 = q4 / 13;
+ int mon = q4 - 13 * q5;
+ int year = 2000 + q5;
+
+ timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
+ }
+
+ if (name.length() >= 9) {
+ region = name.substr(7, 2);
+
+ string xyNum = name.substr(9);
+ unsigned int myXy = m->fromBase36(xyNum);
+ int x = myXy >> 12;
+ int y = myXy & 4095;
+
+ xy = toString(x) + "_" + toString(y);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "decodeName");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
try {
try {
out << ">" << header.name << endl;
- out << "Run Prefix: " << endl;
- out << "Region #: " << endl;
- out << "XY Location: " << endl << endl;
+ out << "Run Prefix: " << header.timestamp << endl;
+ out << "Region #: " << header.region << endl;
+ out << "XY Location: " << header.xy << endl << endl;
out << "Run Name: " << endl;
out << "Analysis Name: " << endl;
exit(1);
}
}
-
+//**********************************************************************************************************************
+bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
+ try {
+ bool okay = true;
+ string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
+
+ if (header.clipQualLeft > read.bases.length()) {
+ okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
+ }
+ if (header.clipQualRight > read.bases.length()) {
+ okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
+ }
+ if (header.clipQualLeft > read.qualScores.size()) {
+ okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
+ }
+ if (header.clipQualRight > read.qualScores.size()) {
+ okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
+ }
+
+ if (okay == false) {
+ m->mothurOut(message); m->mothurOutEndLine();
+ }
+
+ return okay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "sanityCheck");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
try {
-
out << "Flowgram: ";
for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t'; }
for (int i = 0; i < read.flowIndex.size(); i++) { sum += read.flowIndex[i]; out << sum << '\t'; }
//make the bases you want to clip lowercase and the bases you want to keep upper case
+ int endValue = header.clipQualRight;
+ if(endValue == 0){ endValue = read.bases.length(); }
for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
- for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { read.bases[i] = toupper(read.bases[i]); }
- for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) { read.bases[i] = tolower(read.bases[i]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { read.bases[i] = toupper(read.bases[i]); }
+ for (int i = (endValue-1); i < read.bases.length(); i++) { read.bases[i] = tolower(read.bases[i]); }
out << endl << "Bases: " << read.bases << endl << "Quality Scores: ";
for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
//**********************************************************************************************************************
int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
try {
-
string seq = read.bases;
- if (trim) {
- seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft+1));
+ if (trim) {
+ if(header.clipQualRight < header.clipQualLeft){
+ if (header.clipQualRight == 0) { //don't trim right
+ seq = seq.substr(header.clipQualLeft-1);
+ }else {
+ seq = "NNNN";
+ }
+ }
+ else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
+ seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
+ }
+ else {
+ seq = seq.substr(header.clipQualLeft-1);
+ }
}else{
//if you wanted the sfftxt then you already converted the bases to the right case
if (!sfftxt) {
+ int endValue = header.clipQualRight;
//make the bases you want to clip lowercase and the bases you want to keep upper case
+ if(endValue == 0){ endValue = seq.length(); }
for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
- for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { seq[i] = toupper(seq[i]); }
- for (int i = (header.clipQualRight-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
+ for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
}
}
- out << ">" << header.name << endl;
+ out << ">" << header.name << " xy=" << header.xy << endl;
out << seq << endl;
return 0;
try {
if (trim) {
- out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft+1) << endl;
- for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { out << read.qualScores[i] << '\t'; }
+ if(header.clipQualRight < header.clipQualLeft){
+ if (header.clipQualRight == 0) { //don't trim right
+ out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+ }else {
+ out << ">" << header.name << " xy=" << header.xy << endl;
+ out << "0\t0\t0\t0";
+ }
+ }
+ else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
+ out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { out << read.qualScores[i] << '\t'; }
+ }
+ else{
+ out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+ }
}else{
- out << ">" << header.name << " length=" << read.qualScores.size() << endl;
+ out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
}
//**********************************************************************************************************************
int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
try {
+
+ int endValue = header.clipQualRight;
+ if (header.clipQualRight == 0) {
+ endValue = read.flowIndex.size();
+ if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
+ }
+ if(endValue > header.clipQualLeft){
+
+ int rightIndex = 0;
+ for (int i = 0; i < endValue; i++) { rightIndex += read.flowIndex[i]; }
+
+ out << header.name << ' ' << rightIndex;
+ for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100); }
+ out << endl;
+ }
- out << ">" << header.name << endl;
- for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t'; }
- out << endl;
return 0;
}
seqNames.clear();
ifstream in;
- openInputFile(filename, in);
+ m->openInputFile(filename, in);
string name;
while(!in.eof()){
- in >> name; gobble(in);
+ in >> name; m->gobble(in);
seqNames.insert(name);
exit(1);
}
}
-//**********************************************************************************************************************/
+//**********************************************************************************************************************
+int SffInfoCommand::parseSffTxt() {
+ try {
+
+ ifstream inSFF;
+ m->openInputFile(sfftxtFilename, inSFF);
+
+ if (outputDir == "") { outputDir += m->hasPath(sfftxtFilename); }
+
+ //output file names
+ ofstream outFasta, outQual, outFlow;
+ string outFastaFileName, outQualFileName;
+ string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
+ if (fileRoot.length() > 0) {
+ //rip off last .
+ fileRoot = fileRoot.substr(0, fileRoot.length()-1);
+ fileRoot = m->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) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
+ if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
+ if (flow) { m->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 = m->getline(inSFF);
+ string magicNumber = m->getline(inSFF);
+ string version = m->getline(inSFF);
+ string indexOffset = m->getline(inSFF);
+ string indexLength = m->getline(inSFF);
+ int numReads = parseHeaderLineToInt(inSFF);
+ string headerLength = m->getline(inSFF);
+ string keyLength = m->getline(inSFF);
+ int numFlows = parseHeaderLineToInt(inSFF);
+ string flowgramCode = m->getline(inSFF);
+ string flowChars = m->getline(inSFF);
+ string keySequence = m->getline(inSFF);
+ m->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) + "."); m->mothurOutEndLine(); break; }
+
+ Header header;
+
+ //parse read header
+ inSFF >> seqName;
+ seqName = seqName.substr(1);
+ m->gobble(inSFF);
+ header.name = seqName;
+
+ string runPrefix = parseHeaderLineToString(inSFF); header.timestamp = runPrefix;
+ string regionNumber = parseHeaderLineToString(inSFF); header.region = regionNumber;
+ string xyLocation = parseHeaderLineToString(inSFF); header.xy = xyLocation;
+ m->gobble(inSFF);
+
+ string runName = parseHeaderLineToString(inSFF);
+ string analysisName = parseHeaderLineToString(inSFF);
+ string fullPath = parseHeaderLineToString(inSFF);
+ m->gobble(inSFF);
+
+ string readHeaderLen = parseHeaderLineToString(inSFF); convert(readHeaderLen, header.headerLength);
+ string nameLength = parseHeaderLineToString(inSFF); convert(nameLength, header.nameLength);
+ int numBases = parseHeaderLineToInt(inSFF); header.numBases = numBases;
+ string clipQualLeft = parseHeaderLineToString(inSFF); convert(clipQualLeft, header.clipQualLeft);
+ int clipQualRight = parseHeaderLineToInt(inSFF); header.clipQualRight = clipQualRight;
+ string clipAdapLeft = parseHeaderLineToString(inSFF); convert(clipAdapLeft, header.clipAdapterLeft);
+ string clipAdapRight = parseHeaderLineToString(inSFF); convert(clipAdapRight, header.clipAdapterRight);
+ m->gobble(inSFF);
+
+ seqRead read;
+
+ //parse read
+ vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows); read.flowgram = 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.flowIndex = flowIndicesAdjusted;
+
+ string bases = parseHeaderLineToString(inSFF); read.bases = bases;
+ vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases); read.qualScores = qualityScores;
+ m->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(header.name) == 0) { print = false; } }
+
+ //print
+ if (print) {
+ if (fasta) { printFastaSeqData(outFasta, read, header); }
+ if (qual) { printQualSeqData(outQual, read, header); }
+ if (flow) { printFlowSeqData(outFlow, read, header); }
+ }
+
+ //report progress
+ if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
+
+ if (m->control_pressed) { break; }
+ }
+
+ //report progress
+ if (!m->control_pressed) { if((numReads) % 10000 != 0){ m->mothurOut(toString(numReads)); m->mothurOutEndLine(); } }
+
+ 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;
+
+ while (!file.eof()) {
+
+ char c = file.get();
+ if (c == ':'){
+ file >> number;
+ break;
+ }
+
+ }
+ m->gobble(file);
+ return number;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
+ exit(1);
+ }
+
+}
+
+//**********************************************************************************************************************
+
+string SffInfoCommand::parseHeaderLineToString(ifstream& file){
+ try {
+ string text;
+
+ while (!file.eof()) {
+ char c = file.get();
+
+ if (c == ':'){
+ //m->gobble(file);
+ //text = m->getline(file);
+ file >> text;
+ break;
+ }
+ }
+ m->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;
+ }
+ }
+ m->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;
+ }
+ }
+ m->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();
+
+ ifstream inOligos;
+ m->openInputFile(oligoFile, inOligos);
+
+ string type, oligo, group;
+
+ int indexPrimer = 0;
+ int indexBarcode = 0;
+
+ while(!inOligos.eof()){
+
+ inOligos >> type;
+
+ if(type[0] == '#'){
+ while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ m->gobble(inOligos);
+ }
+ else{
+ m->gobble(inOligos);
+ //make type case insensitive
+ for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
+
+ inOligos >> oligo;
+
+ for(int i=0;i<oligo.length();i++){
+ oligo[i] = toupper(oligo[i]);
+ if(oligo[i] == 'U') { oligo[i] = 'T'; }
+ }
+
+ if(type == "FORWARD"){
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ //check for repeat barcodes
+ map<string, int>::iterator itPrime = primers.find(oligo);
+ if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ primers[oligo]=indexPrimer; indexPrimer++;
+ primerNameVector.push_back(group);
+ }else if(type == "REVERSE"){
+ //Sequence oligoRC("reverse", oligo);
+ //oligoRC.reverseComplement();
+ string oligoRC = reverseOligo(oligo);
+ revPrimer.push_back(oligoRC);
+ }
+ else if(type == "BARCODE"){
+ inOligos >> group;
+
+ //check for repeat barcodes
+ map<string, int>::iterator itBar = barcodes.find(oligo);
+ if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ barcodes[oligo]=indexBarcode; indexBarcode++;
+ barcodeNameVector.push_back(group);
+ }else if(type == "LINKER"){
+ linker.push_back(oligo);
+ }else if(type == "SPACER"){
+ spacer.push_back(oligo);
+ }
+ else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
+ }
+ m->gobble(inOligos);
+ }
+ inOligos.close();
+
+ if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ split = 1; }
+
+ //add in potential combos
+ if(barcodeNameVector.size() == 0){
+ barcodes[""] = 0;
+ barcodeNameVector.push_back("");
+ }
+
+ if(primerNameVector.size() == 0){
+ primers[""] = 0;
+ primerNameVector.push_back("");
+ }
+
+ filehandles.resize(barcodeNameVector.size());
+ for(int i=0;i<filehandles.size();i++){
+ filehandles[i].assign(primerNameVector.size(), "");
+ }
+
+ if(split > 1){
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ 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 = primerNameVector[itPrimer->second];
+ string barcodeName = barcodeNameVector[itBar->second];
+
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ }
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+ variables["[group]"] = comboGroupName;
+ string thisFilename = getOutputFileName("sff",variables);
+ if (uniqueNames.count(thisFilename) == 0) {
+ outputNames.push_back(thisFilename);
+ outputTypes["sff"].push_back(thisFilename);
+ uniqueNames.insert(thisFilename);
+ }
+
+ filehandles[itBar->second][itPrimer->second] = thisFilename;
+ m->openOutputFile(thisFilename, temp); temp.close();
+ }
+ }
+ }
+ numFPrimers = primers.size();
+ numLinkers = linker.size();
+ numSpacers = spacer.size();
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+ variables["[group]"] = "scrap";
+ noMatchFile = getOutputFileName("sff",variables);
+ m->mothurRemove(noMatchFile);
+
+ bool allBlank = true;
+ for (int i = 0; i < barcodeNameVector.size(); i++) {
+ if (barcodeNameVector[i] != "") {
+ allBlank = false;
+ break;
+ }
+ }
+ for (int i = 0; i < primerNameVector.size(); i++) {
+ if (primerNameVector[i] != "") {
+ allBlank = false;
+ break;
+ }
+ }
+
+ 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");
+ }
+ }
+
+ if (allBlank) {
+ m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a split the sff file."); m->mothurOutEndLine();
+ split = 1;
+ return false;
+ }
+
+ return true;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "readOligos");
+ exit(1);
+ }
+}
+//********************************************************************/
+string SffInfoCommand::reverseOligo(string oligo){
+ try {
+ string reverse = "";
+
+ for(int i=oligo.length()-1;i>=0;i--){
+
+ if(oligo[i] == 'A') { reverse += 'T'; }
+ else if(oligo[i] == 'T'){ reverse += 'A'; }
+ else if(oligo[i] == 'U'){ reverse += 'A'; }
+
+ else if(oligo[i] == 'G'){ reverse += 'C'; }
+ else if(oligo[i] == 'C'){ reverse += 'G'; }
+
+ else if(oligo[i] == 'R'){ reverse += 'Y'; }
+ else if(oligo[i] == 'Y'){ reverse += 'R'; }
+
+ else if(oligo[i] == 'M'){ reverse += 'K'; }
+ else if(oligo[i] == 'K'){ reverse += 'M'; }
+
+ else if(oligo[i] == 'W'){ reverse += 'W'; }
+ else if(oligo[i] == 'S'){ reverse += 'S'; }
+
+ else if(oligo[i] == 'B'){ reverse += 'V'; }
+ else if(oligo[i] == 'V'){ reverse += 'B'; }
+
+ else if(oligo[i] == 'D'){ reverse += 'H'; }
+ else if(oligo[i] == 'H'){ reverse += 'D'; }
+
+ else { reverse += 'N'; }
+ }
+
+
+ return reverse;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "reverseOligo");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
+
projects / mothur.git / blobdiff