+++ /dev/null
-/*
- * sffinfocommand.cpp
- * Mothur
- *
- * Created by westcott on 7/7/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "sffinfocommand.h"
-#include "endiannessmacros.h"
-
-//**********************************************************************************************************************
-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", "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, 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", "getHelpString");
- 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;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-SffInfoCommand::SffInfoCommand(string option) {
- try {
- abort = false; calledHelp = false;
- hasAccnos = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- //valid paramters for this command
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string, string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- //check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
- 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;
-
- //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 = ""; }
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; }
-
- sffFilename = validParameter.validFile(parameters, "sff", false);
- 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++) {
- 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 (!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]); }
- }
- }
-
- //make sure there is at least one valid file left
- if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
- }
-
- accnosName = validParameter.validFile(parameters, "accnos", false);
- if (accnosName == "not found") { accnosName = ""; }
- else {
- hasAccnos = true;
- 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++) {
- 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 (!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; }
- }
-
- 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 = m->isTrue(temp);
-
- 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 = "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 = 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) {
- m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SffInfoCommand::execute(){
- try {
- 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++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- int start = time(NULL);
-
- m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
-
- string accnos = "";
- if (hasAccnos) { accnos = accnosFileNames[s]; }
-
- int numReads = extractSffInfo(filenames[s], accnos);
-
- m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
- }
-
- 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();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SffInfoCommand::extractSffInfo(string input, string accnos){
- try {
-
- if (outputDir == "") { outputDir += m->hasPath(input); }
-
- if (accnos != "") { readAccnosFile(accnos); }
- else { seqNames.clear(); }
-
- ofstream outSfftxt, outFasta, outQual, outFlow;
- string outFastaFileName, outQualFileName;
- string rootName = outputDir + m->getRootName(m->getSimpleName(input));
- if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
-
- string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
- string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
- if (trim) {
- outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
- }else{
- outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
- }
-
- 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 (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);
- 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; } }
-
- //print
- if (print) {
- if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
- if (fasta) { printFastaSeqData(outFasta, read, readheader); }
- if (qual) { printQualSeqData(outQual, read, readheader); }
- if (flow) { printFlowSeqData(outFlow, read, readheader); }
- }
-
- count++;
- mycount++;
-
- //report progress
- if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
-
- if (m->control_pressed) { count = 0; break; }
-
- if (count >= header.numReads) { break; }
- }
-
- //report progress
- if (!m->control_pressed) { if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
-
- in.close();
-
- if (sfftxt) { outSfftxt.close(); }
- if (fasta) { outFasta.close(); }
- if (qual) { outQual.close(); }
- if (flow) { outFlow.close(); }
-
- return count;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "extractSffInfo");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-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])); }
-
- //read offset
- char buffer2 [8];
- in.read(buffer2, 8);
- 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.numReads = be_int4(*(unsigned int *)(&buffer4));
-
- //read header length
- char buffer5 [2];
- in.read(buffer5, 2);
- header.headerLength = be_int2(*(unsigned short *)(&buffer5));
-
- //read key length
- char buffer6 [2];
- in.read(buffer6, 2);
- header.keyLength = be_int2(*(unsigned short *)(&buffer6));
-
- //read number of flow reads
- char buffer7 [2];
- in.read(buffer7, 2);
- header.numFlowsPerRead = be_int2(*(unsigned short *)(&buffer7));
-
- //read format code
- char buffer8 [1];
- in.read(buffer8, 1);
- header.flogramFormatCode = (int)(buffer8[0]);
-
- //read flow chars
- char* tempBuffer = new char[header.numFlowsPerRead];
- in.read(&(*tempBuffer), header.numFlowsPerRead);
- header.flowChars = tempBuffer;
- if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead); }
- delete[] tempBuffer;
-
- //read key
- char* tempBuffer2 = new char[header.keyLength];
- in.read(&(*tempBuffer2), header.keyLength);
- 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 long spotInFile = in.tellg();
- unsigned long long spot = (spotInFile + 7)& ~7; // ~ inverts
- in.seekg(spot);
-
- }else{
- m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "readCommonHeader");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SffInfoCommand::readHeader(ifstream& in, Header& header){
- try {
-
- if (!in.eof()) {
-
- //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);
- header.numBases = be_int4(*(unsigned int *)(&buffer3));
-
- //read clip qual left
- 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));
-
- //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);
- header.name = tempBuffer;
- 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 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()) {
-
- //read flowgram
- read.flowgram.resize(numFlowReads);
- for (int i = 0; i < numFlowReads; i++) {
- char buffer [2];
- 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++) {
- 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;
-
- //read qual scores
- read.qualScores.resize(numBases);
- for (int i = 0; i < numBases; i++) {
- char temp[1];
- in.read(temp, 1);
- read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
- }
-
- /* Pad to 8 chars */
- unsigned long long spotInFile = in.tellg();
- unsigned long long spot = (spotInFile + 7)& ~7;
- in.seekg(spot);
-
- }else{
- m->mothurOut("Error reading."); m->mothurOutEndLine();
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "readSeqData");
- 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 {
-
- out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
- out << "Version: " << header.version << endl;
- out << "Index Offset: " << header.indexOffset << endl;
- out << "Index Length: " << header.indexLength << endl;
- out << "Number of Reads: " << header.numReads << endl;
- out << "Header Length: " << header.headerLength << endl;
- out << "Key Length: " << header.keyLength << endl;
- out << "Number of Flows: " << header.numFlowsPerRead << endl;
- out << "Format Code: " << header.flogramFormatCode << endl;
- out << "Flow Chars: " << header.flowChars << endl;
- out << "Key Sequence: " << header.keySequence << endl << endl;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printCommonHeader");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SffInfoCommand::printHeader(ofstream& out, Header& header) {
- try {
-
- out << ">" << header.name << 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;
- out << "Full Path: " << endl << endl;
-
- out << "Read Header Len: " << header.headerLength << endl;
- out << "Name Length: " << header.nameLength << endl;
- out << "# of Bases: " << header.numBases << endl;
- out << "Clip Qual Left: " << header.clipQualLeft << endl;
- out << "Clip Qual Right: " << header.clipQualRight << endl;
- out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
- out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printHeader");
- 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'; }
-
- out << endl << "Flow Indexes: ";
- int sum = 0;
- 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
- if(header.clipQualRight == 0){ header.clipQualRight = 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]); }
-
- out << endl << "Bases: " << read.bases << endl << "Quality Scores: ";
- for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
-
-
- out << endl << endl;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
- try {
- string seq = read.bases;
-
- if (trim) {
- if(header.clipQualRight < header.clipQualLeft){
- 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) {
- //make the bases you want to clip lowercase and the bases you want to keep upper case
- if(header.clipQualRight == 0){ header.clipQualRight = 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]); }
- }
- }
-
- out << ">" << header.name << " xy=" << header.xy << endl;
- out << seq << endl;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
- try {
-
- 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 << " 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 << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
- for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
- }
-
- out << endl;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printQualSeqData");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-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;
- }
-
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SffInfoCommand::readAccnosFile(string filename) {
- try {
- //remove old names
- seqNames.clear();
-
- ifstream in;
- m->openInputFile(filename, in);
- string name;
-
- while(!in.eof()){
- in >> name; m->gobble(in);
-
- seqNames.insert(name);
-
- if (m->control_pressed) { seqNames.clear(); break; }
- }
- in.close();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "readAccnosFile");
- 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