X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sffinfocommand.cpp;h=e2527ff3bc0bd7be5caa6124b6594bc172574e13;hp=01338ca34be42556131b15a0ead73c0ef9952858;hb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;hpb=fbaa6c7ac44f857c1ece7c8199e9e7e09b4bbe74 diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp index 01338ca..e2527ff 100644 --- a/sffinfocommand.cpp +++ b/sffinfocommand.cpp @@ -1,655 +1,674 @@ -/* - * sffinfocommand.cpp - * Mothur - * - * Created by westcott on 7/7/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "sffinfocommand.h" -#include "endiannessmacros.h" - -//********************************************************************************************************************** - -SffInfoCommand::SffInfoCommand(string option) { - try { - abort = false; - hasAccnos = false; - - //allow user to run help - if(option == "help") { help(); abort = true; } - - else { - //valid paramters for this command - string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - //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") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true; } - else { - 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; - } - } - 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--; - } - } - - //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; - 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]; } - } - - ifstream in; - int ableToOpen = 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() + getSimpleName(accnosFileNames[i]); - m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); - 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 = isTrue(temp); - - temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; } - fasta = isTrue(temp); - - temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; } - flow = isTrue(temp); - - temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; } - trim = isTrue(temp); - - temp = validParameter.validFile(parameters, "sfftxt", false); if (temp == "not found"){ temp = "F"; } - sfftxt = isTrue(temp); - } - } - catch(exception& e) { - m->errorOut(e, "SffInfoCommand", "SffInfoCommand"); - 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; } - - 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; } - - 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 (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - - //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 += hasPath(input); } - - if (accnos != "") { readAccnosFile(accnos); } - else { seqNames.clear(); } - - 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); } - - ifstream in; - in.open(input.c_str(), ios::binary); - - CommonHeader header; - readCommonHeader(in, header); - - int count = 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); } - - //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); - - //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); } - if (fasta) { printFastaSeqData(outFasta, read, readheader); } - if (qual) { printQualSeqData(outQual, read, readheader); } - if (flow) { printFlowSeqData(outFlow, read, readheader); } - } - - count++; - - //report progress - if((count+1) % 500 == 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) % 500 != 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[sizeof(header.magicNumber)]; - in.read(buffer, sizeof(header.magicNumber)); - 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 [sizeof(header.indexOffset)]; - in.read(buffer2, sizeof(header.indexOffset)); - header.indexOffset = be_int8(*(unsigned long int *)(&buffer2)); - - //read index length - char buffer3 [sizeof(header.indexLength)]; - in.read(buffer3, sizeof(header.indexLength)); - header.indexLength = be_int4(*(unsigned int *)(&buffer3)); - - //read num reads - char buffer4 [sizeof(header.numReads)]; - in.read(buffer4, sizeof(header.numReads)); - header.numReads = be_int4(*(unsigned int *)(&buffer4)); - - //read header length - char buffer5 [sizeof(header.headerLength)]; - in.read(buffer5, sizeof(header.headerLength)); - header.headerLength = be_int2(*(unsigned short *)(&buffer5)); - - //read key length - char buffer6 [sizeof(header.keyLength)]; - in.read(buffer6, sizeof(header.keyLength)); - header.keyLength = be_int2(*(unsigned short *)(&buffer6)); - - //read number of flow reads - char buffer7 [sizeof(header.numFlowsPerRead)]; - in.read(buffer7, sizeof(header.numFlowsPerRead)); - 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 [header.numFlowsPerRead]; - in.read(tempBuffer, header.numFlowsPerRead); - header.flowChars = tempBuffer; - if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead); } - - //read key - char tempBuffer2 [header.keyLength]; - in.read(tempBuffer2, header.keyLength); - header.keySequence = tempBuffer2; - if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength); } - - /* Pad to 8 chars */ - unsigned long int spotInFile = in.tellg(); - unsigned long int 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 [sizeof(header.headerLength)]; - in.read(buffer, sizeof(header.headerLength)); - header.headerLength = be_int2(*(unsigned short *)(&buffer)); - - //read name length - char buffer2 [sizeof(header.nameLength)]; - in.read(buffer2, sizeof(header.nameLength)); - header.nameLength = be_int2(*(unsigned short *)(&buffer2)); - - //read num bases - char buffer3 [sizeof(header.numBases)]; - in.read(buffer3, sizeof(header.numBases)); - header.numBases = be_int4(*(unsigned int *)(&buffer3)); - - //read clip qual left - char buffer4 [sizeof(header.clipQualLeft)]; - in.read(buffer4, sizeof(header.clipQualLeft)); - header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4)); - - //read clip qual right - char buffer5 [sizeof(header.clipQualRight)]; - in.read(buffer5, sizeof(header.clipQualRight)); - header.clipQualRight = be_int2(*(unsigned short *)(&buffer5)); - - //read clipAdapterLeft - char buffer6 [sizeof(header.clipAdapterLeft)]; - in.read(buffer6, sizeof(header.clipAdapterLeft)); - header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6)); - - //read clipAdapterRight - char buffer7 [sizeof(header.clipAdapterRight)]; - in.read(buffer7, sizeof(header.clipAdapterRight)); - header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7)); - - //read name - char tempBuffer [header.nameLength]; - in.read(tempBuffer, header.nameLength); - header.name = tempBuffer; - if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength); } - - /* Pad to 8 chars */ - unsigned long int spotInFile = in.tellg(); - unsigned long int 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 [sizeof(unsigned short)]; - in.read(buffer, (sizeof(unsigned short))); - 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[numBases]; - in.read(tempBuffer, numBases); - read.bases = tempBuffer; - if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases); } - - //read flowgram - 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 int spotInFile = in.tellg(); - unsigned long int 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::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: " << endl; - out << "Region #: " << endl; - out << "XY Location: " << 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); - } -} - -//********************************************************************************************************************** -int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read) { - 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'; } - - 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) { - seq = seq.substr(header.clipQualLeft, (header.clipQualRight-header.clipQualLeft)); - } - - out << ">" << header.name << 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) { - out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl; - for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) { out << read.qualScores[i] << '\t'; } - }else{ - out << ">" << header.name << " 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 { - - 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; - } - catch(exception& e) { - m->errorOut(e, "SffInfoCommand", "printFlowSeqData"); - exit(1); - } -} -//********************************************************************************************************************** -int SffInfoCommand::readAccnosFile(string filename) { - try { - //remove old names - seqNames.clear(); - - ifstream in; - openInputFile(filename, in); - string name; - - while(!in.eof()){ - in >> name; 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); - } -} -//**********************************************************************************************************************/ +/* + * sffinfocommand.cpp + * Mothur + * + * Created by westcott on 7/7/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "sffinfocommand.h" +#include "endiannessmacros.h" + +//********************************************************************************************************************** + +SffInfoCommand::SffInfoCommand(string option) { + try { + abort = false; + hasAccnos = false; + + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //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") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true; } + else { + 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; + } + } + 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--; + } + } + + //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; + 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]; } + } + + ifstream in; + int ableToOpen = 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() + getSimpleName(accnosFileNames[i]); + m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ableToOpen = openInputFile(tryPath, in, "noerror"); + 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 = isTrue(temp); + + temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; } + fasta = isTrue(temp); + + temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; } + flow = isTrue(temp); + + temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; } + trim = isTrue(temp); + + temp = validParameter.validFile(parameters, "sfftxt", false); if (temp == "not found"){ temp = "F"; } + sfftxt = isTrue(temp); + } + } + catch(exception& e) { + m->errorOut(e, "SffInfoCommand", "SffInfoCommand"); + 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; } + + 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; } + + 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 (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + + //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 += hasPath(input); } + + if (accnos != "") { readAccnosFile(accnos); } + else { seqNames.clear(); } + + 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); } + + ifstream in; + in.open(input.c_str(), ios::binary); + + CommonHeader header; + readCommonHeader(in, header); + + int count = 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); } + + //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); + + //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++; + + //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 int *)(&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 int spotInFile = in.tellg(); + unsigned long int 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)); + + //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; + + /* Pad to 8 chars */ + unsigned long int spotInFile = in.tellg(); + unsigned long int 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 int spotInFile = in.tellg(); + unsigned long int 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::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: " << endl; + out << "Region #: " << endl; + out << "XY Location: " << 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); + } +} + +//********************************************************************************************************************** +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 + for (int i = 0; i < header.clipQualLeft; i++) { read.bases[i] = tolower(read.bases[i]); } + for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) { read.bases[i] = toupper(read.bases[i]); } + for (int i = (header.clipQualRight-header.clipQualLeft); 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) { + seq = seq.substr(header.clipQualLeft, (header.clipQualRight-header.clipQualLeft)); + }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 + for (int i = 0; i < header.clipQualLeft; i++) { seq[i] = tolower(seq[i]); } + for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) { seq[i] = toupper(seq[i]); } + for (int i = (header.clipQualRight-header.clipQualLeft); i < seq.length(); i++) { seq[i] = tolower(seq[i]); } + } + } + + out << ">" << header.name << 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) { + out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl; + for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) { out << read.qualScores[i] << '\t'; } + }else{ + out << ">" << header.name << " 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 { + + 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; + } + catch(exception& e) { + m->errorOut(e, "SffInfoCommand", "printFlowSeqData"); + exit(1); + } +} +//********************************************************************************************************************** +int SffInfoCommand::readAccnosFile(string filename) { + try { + //remove old names + seqNames.clear(); + + ifstream in; + openInputFile(filename, in); + string name; + + while(!in.eof()){ + in >> name; 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); + } +} +//**********************************************************************************************************************/