X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=20caead668196fc75d10de1275956b7955bdd3b6;hb=01f6af90c907264686304a5c684c702e94ff40ae;hp=4965cfd75e06c9f8ba8157056922514581e3e10e;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp index 4965cfd..20caead 100644 --- a/sffinfocommand.cpp +++ b/sffinfocommand.cpp @@ -16,7 +16,7 @@ vector SffInfoCommand::setParameters(){ 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", "", "F", "", "", "",false,false); parameters.push_back(pflow); + 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); @@ -41,7 +41,7 @@ string SffInfoCommand::getHelpString(){ 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=False. \n"; + helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated. Default=True. \n"; helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. Default=False. \n"; helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n"; helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. Default=True. \n"; @@ -256,7 +256,7 @@ SffInfoCommand::SffInfoCommand(string option) { 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"; } @@ -298,7 +298,6 @@ SffInfoCommand::SffInfoCommand(string option) { //********************************************************************************************************************** int SffInfoCommand::execute(){ try { - if (abort == true) { if (calledHelp) { return 0; } return 2; } for (int s = 0; s < filenames.size(); s++) { @@ -362,6 +361,9 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){ 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) { @@ -406,7 +408,9 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){ //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; } } @@ -609,7 +613,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i in.read(buffer, 2); read.flowgram[i] = be_int2(*(unsigned short *)(&buffer)); } - + //read flowIndex read.flowIndex.resize(numBases); for (int i = 0; i < numBases; i++) { @@ -741,11 +745,39 @@ int SffInfoCommand::printHeader(ofstream& out, Header& header) { 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'; } @@ -775,10 +807,9 @@ int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& hea //********************************************************************************************************************** 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"; }