#include "endiannessmacros.h"
//**********************************************************************************************************************
-vector<string> SffInfoCommand::getValidParameters(){
- try {
- string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+vector<string> SffInfoCommand::setParameters(){
+ try {
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
+ 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", "", "", "",false,false); parameters.push_back(pflow);
+ CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
+ CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
+ CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
+ 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", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SffInfoCommand::SffInfoCommand(){
- try {
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["flow"] = tempOutNames;
- outputTypes["sfftxt"] = tempOutNames;
- outputTypes["qual"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
+ m->errorOut(e, "SffInfoCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SffInfoCommand::getRequiredParameters(){
+string SffInfoCommand::getHelpString(){
try {
- string Array[] = {"sff"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ 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, 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 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", "getRequiredParameters");
+ m->errorOut(e, "SffInfoCommand", "getHelpString");
exit(1);
}
}
+
+
//**********************************************************************************************************************
-vector<string> SffInfoCommand::getRequiredFiles(){
+SffInfoCommand::SffInfoCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
+ outputTypes["sfftxt"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "getRequiredFiles");
+ m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
exit(1);
}
}
SffInfoCommand::SffInfoCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
hasAccnos = false;
//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();
outputTypes["fasta"] = tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["sfftxt"] = tempOutNames;
- outputTypes["qual"] = tempOutNames;
+ outputTypes["qfile"] = 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 {
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 = 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;
+ 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--;
}
}
- //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;
+ 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]; }
}
- }
-
- in.close();
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
- 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 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]); }
}
}
//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 = 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;
+ 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--;
}
}
- //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;
+
+ 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]; }
}
- }
- in.close();
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
- 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 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--;
+ }
}
}
temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; }
fasta = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; }
+ 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 = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "sfftxt", false); if (temp == "not found"){ temp = "F"; }
- sfftxt = m->isTrue(temp);
+ 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);
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();
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["qual"].push_back(outQualFileName); }
- if (flow) { m->openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outputTypes["flow"].push_back(outFlowFileName); }
+ 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()) {
//read data
seqRead read;
readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
-
+ 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(); }
//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];
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{
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{
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++) {
}
/* 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{
}
}
//**********************************************************************************************************************
+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'; }
//**********************************************************************************************************************
int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
try {
-
string seq = read.bases;
- if (trim) {
+ if (trim) {
if(header.clipQualRight < header.clipQualLeft){
seq = "NNNN";
}
}
}
- out << ">" << header.name << endl;
+ out << ">" << header.name << " xy=" << header.xy << endl;
out << seq << endl;
return 0;
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
+ 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 << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ 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 << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ 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 {
+ if(header.clipQualRight > header.clipQualLeft){
+
+ int rightIndex = 0;
+ for (int i = 0; i < header.clipQualRight; 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;
}
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);
+ }
+
+ string outFlowFileName = outputDir + fileRoot + "flow";
+ if (trim) {
+ outFastaFileName = outputDir + fileRoot + "fasta";
+ outQualFileName = outputDir + fileRoot + "qual";
+ }else{
+ outFastaFileName = outputDir + fileRoot + "raw.fasta";
+ outQualFileName = outputDir + fileRoot + "raw.qual";
+ }
+
+ 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["qual"].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);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
+
projects / mothur.git / blobdiff