X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=392f5877d9099308593d0cba26a8ff7baddd1d3b;hb=2405cc589aaaf0c44809a48fe98d3b96863dac0b;hp=407850f6ef80ac0c0d47811b785873d67f03e319;hpb=6973be461c47c057531f447de22003a30cabc193;p=mothur.git diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp index 407850f..392f587 100644 --- a/seqerrorcommand.cpp +++ b/seqerrorcommand.cpp @@ -13,14 +13,39 @@ #include "refchimeratest.h" //********************************************************************************************************************** -vector SeqErrorCommand::getValidParameters(){ +vector SeqErrorCommand::setParameters(){ try { - string Array[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pquery); + CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(preference); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(pqfile); + CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(preport); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras); + CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "SeqErrorCommand", "getValidParameters"); + m->errorOut(e, "SeqErrorCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string SeqErrorCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n"; + helpString += "Example seq.error(...).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "SeqErrorCommand", "getHelpString"); exit(1); } } @@ -44,29 +69,6 @@ SeqErrorCommand::SeqErrorCommand(){ exit(1); } } -//********************************************************************************************************************** -vector SeqErrorCommand::getRequiredParameters(){ - try { - string Array[] = {"query","reference"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "SeqErrorCommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector SeqErrorCommand::getRequiredFiles(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "SeqErrorCommand", "getRequiredFiles"); - exit(1); - } -} //*************************************************************************************************************** SeqErrorCommand::SeqErrorCommand(string option) { @@ -79,11 +81,7 @@ SeqErrorCommand::SeqErrorCommand(string option) { else { string temp; - - //valid paramters for this command - string AlignArray[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "ignorechimeras", "outputdir"}; - - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -114,12 +112,12 @@ SeqErrorCommand::SeqErrorCommand(string option) { if (inputDir == "not found"){ inputDir = ""; } else { string path; - it = parameters.find("query"); + it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["query"] = inputDir + it->second; } + if (path == "") { parameters["fasta"] = inputDir + it->second; } } it = parameters.find("reference"); @@ -156,8 +154,12 @@ SeqErrorCommand::SeqErrorCommand(string option) { } //check for required parameters - queryFileName = validParameter.validFile(parameters, "query", true); - if (queryFileName == "not found") { m->mothurOut("query is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; } + queryFileName = validParameter.validFile(parameters, "fasta", true); + if (queryFileName == "not found") { + queryFileName = m->getFastaFile(); + if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + } else if (queryFileName == "not open") { abort = true; } referenceFileName = validParameter.validFile(parameters, "reference", true); @@ -168,12 +170,15 @@ SeqErrorCommand::SeqErrorCommand(string option) { //check for optional parameters namesFileName = validParameter.validFile(parameters, "name", true); if(namesFileName == "not found"){ namesFileName = ""; } + else if (namesFileName == "not open") { namesFileName = ""; abort = true; } qualFileName = validParameter.validFile(parameters, "qfile", true); if(qualFileName == "not found"){ qualFileName = ""; } + else if (qualFileName == "not open") { qualFileName = ""; abort = true; } reportFileName = validParameter.validFile(parameters, "report", true); if(reportFileName == "not found"){ reportFileName = ""; } + else if (reportFileName == "not open") { reportFileName = ""; abort = true; } if((reportFileName != "" && qualFileName == "") || (reportFileName == "" && qualFileName != "")){ m->mothurOut("if you use either a qual file or a report file, you have to have both."); @@ -204,32 +209,14 @@ SeqErrorCommand::SeqErrorCommand(string option) { exit(1); } } - -//********************************************************************************************************************** - -void SeqErrorCommand::help(){ - try { - m->mothurOut("The seq.error command reads a query alignment file and a reference alignment file and creates .....\n"); - m->mothurOut("Example seq.error(...).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"); - m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n\n"); - } - catch(exception& e) { - m->errorOut(e, "SeqErrorCommand", "help"); - exit(1); - } -} - -//*************************************************************************************************************** - -SeqErrorCommand::~SeqErrorCommand(){ /* void */ } - //*************************************************************************************************************** int SeqErrorCommand::execute(){ try{ if (abort == true) { if (calledHelp) { return 0; } return 2; } + maxLength = 2000; + string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary"; m->openOutputFile(errorSummaryFileName, errorSummaryFile); outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName); @@ -259,11 +246,11 @@ int SeqErrorCommand::execute(){ m->openInputFile(qualFileName, qualFile); report = ReportFile(reportFile, reportFileName); - qualForwardMap.resize(1000); - qualReverseMap.resize(1000); - for(int i=0;i<1000;i++){ - qualForwardMap[i].assign(100,0); - qualReverseMap[i].assign(100,0); + qualForwardMap.resize(maxLength); + qualReverseMap.resize(maxLength); + for(int i=0;i > errorForward; - errorForward['m'].assign(1000,0); - errorForward['s'].assign(1000,0); - errorForward['i'].assign(1000,0); - errorForward['d'].assign(1000,0); - errorForward['a'].assign(1000,0); + errorForward['m'].assign(maxLength,0); + errorForward['s'].assign(maxLength,0); + errorForward['i'].assign(maxLength,0); + errorForward['d'].assign(maxLength,0); + errorForward['a'].assign(maxLength,0); map > errorReverse; - errorReverse['m'].assign(1000,0); - errorReverse['s'].assign(1000,0); - errorReverse['i'].assign(1000,0); - errorReverse['d'].assign(1000,0); - errorReverse['a'].assign(1000,0); + errorReverse['m'].assign(maxLength,0); + errorReverse['s'].assign(maxLength,0); + errorReverse['i'].assign(maxLength,0); + errorReverse['d'].assign(maxLength,0); + errorReverse['a'].assign(maxLength,0); string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera"; @@ -326,10 +313,10 @@ int SeqErrorCommand::execute(){ else{ minCompare.weight = 1; } printErrorData(minCompare, numParentSeqs); - + if(!ignoreSeq){ - - for(int i=0;iopenOutputFile(errorCountFileName, errorCountFile); outputNames.push_back(errorCountFileName); outputTypes["error.count"].push_back(errorCountFileName); - m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n\n"); + m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n"); m->mothurOut("Errors\tSequences\n"); errorCountFile << "Errors\tSequences\n"; for(int i=0;i 0){ numAmbigSeqs++; } - int startPos = currentSeq.getStartPos(); - if(startPos > maxStartPos) { maxStartPos = startPos; } - - int endPos = currentSeq.getEndPos(); - if(endPos < minEndPos) { minEndPos = endPos; } +// int startPos = currentSeq.getStartPos(); +// if(startPos > maxStartPos) { maxStartPos = startPos; } +// +// int endPos = currentSeq.getEndPos(); +// if(endPos < minEndPos) { minEndPos = endPos; } referenceSeqs.push_back(currentSeq); + m->gobble(referenceFile); } referenceFile.close(); @@ -716,7 +704,7 @@ void SeqErrorCommand::printErrorFRFile(map > errorForward, map outputNames.push_back(errorForwardFileName); outputTypes["error.forward"].push_back(errorForwardFileName); errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl; - for(int i=0;i<1000;i++){ + for(int i=0;i > errorForward, map outputNames.push_back(errorReverseFileName); outputTypes["error.reverse"].push_back(errorReverseFileName); errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl; - for(int i=0;i<1000;i++){ + for(int i=0;i > qScoreErrorMap){ //*************************************************************************************************************** void SeqErrorCommand::printQualityFR(vector > qualForwardMap, vector > qualReverseMap){ - try{ - - int lastRow = 0; - int lastColumn = 0; + try{ + int numRows = 0; + int numColumns = qualForwardMap[0].size(); for(int i=0;i > qualForwardMap, vector m->openOutputFile(qualityForwardFileName, qualityForwardFile); outputNames.push_back(qualityForwardFileName); outputTypes["error.qual.forward"].push_back(qualityForwardFileName); - for(int i=0;i > qualForwardMap, vector m->openOutputFile(qualityReverseFileName, qualityReverseFile); outputNames.push_back(qualityReverseFileName); outputTypes["error.qual.reverse"].push_back(qualityReverseFileName); - for(int i=0;i > qualForwardMap, vector m->errorOut(e, "SeqErrorCommand", "printErrorFRFile"); exit(1); } + } - //***************************************************************************************************************