X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;h=4cec90f567c764e8770987c150b67b5ececc0d35;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=6e43b1025cae8ccc828e7e48c51b63304200dc62;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;p=mothur.git diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp index 6e43b10..4cec90f 100644 --- a/removelineagecommand.cpp +++ b/removelineagecommand.cpp @@ -12,54 +12,91 @@ #include "listvector.hpp" //********************************************************************************************************************** -vector RemoveLineageCommand::getValidParameters(){ +vector RemoveLineageCommand::setParameters(){ try { - string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist); + CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy); + CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport); + CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon); + CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups); + 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, "RemoveLineageCommand", "getValidParameters"); + m->errorOut(e, "RemoveLineageCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -RemoveLineageCommand::RemoveLineageCommand(){ +string RemoveLineageCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["taxonomy"] = tempOutNames; - outputTypes["name"] = tempOutNames; - outputTypes["group"] = tempOutNames; - outputTypes["alignreport"] = tempOutNames; - outputTypes["list"] = tempOutNames; + string helpString = ""; + helpString += "The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n"; + helpString += "It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n"; + helpString += "The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy unless you have a valid current taxonomy file.\n"; + helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n"; + helpString += "The taxon parameter allows you to select the taxons you would like to remove, and is required.\n"; + helpString += "You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n"; + helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n"; + helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n"; + helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n"; + helpString += "Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n"; + helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand"); + m->errorOut(e, "RemoveLineageCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector RemoveLineageCommand::getRequiredParameters(){ +string RemoveLineageCommand::getOutputFileNameTag(string type, string inputName=""){ try { - string Array[] = {"taxonomy"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "alignreport") { outputFileName = "pick.align.report"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; } catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "getRequiredParameters"); + m->errorOut(e, "RemoveLineageCommand", "getOutputFileNameTag"); exit(1); } } //********************************************************************************************************************** -vector RemoveLineageCommand::getRequiredFiles(){ +RemoveLineageCommand::RemoveLineageCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["list"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "getRequiredFiles"); + m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand"); exit(1); } } @@ -70,11 +107,10 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { //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 - string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -156,16 +192,19 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } + if (fastafile == "not open") { fastafile = ""; abort = true; } else if (fastafile == "not found") { fastafile = ""; } + else { m->setFastaFile(fastafile); } namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not open") { abort = true; } + if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } @@ -174,10 +213,15 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } else if (listfile == "not found") { listfile = ""; } + else { m->setListFile(listfile); } taxfile = validParameter.validFile(parameters, "taxonomy", true); - if (taxfile == "not open") { abort = true; } - else if (taxfile == "not found") { taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine(); abort = true; } + if (taxfile == "not open") { taxfile = ""; abort = true; } + else if (taxfile == "not found") { + taxfile = m->getTaxonomyFile(); + if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setTaxonomyFile(taxfile); } string usedDups = "true"; string temp = validParameter.validFile(parameters, "dups", false); @@ -194,12 +238,17 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { if (taxons[0] == '\'') { taxons = taxons.substr(1); } if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); } } - + m->splitAtChar(taxons, listOfTaxons, '-'); if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; } if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; } - + + if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } + } } @@ -210,29 +259,6 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { } //********************************************************************************************************************** -void RemoveLineageCommand::help(){ - try { - m->mothurOut("The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n"); - m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n"); - m->mothurOut("The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy and taxon.\n"); - m->mothurOut("The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n"); - m->mothurOut("The taxon parameter allows you to select the taxons you would like to remove.\n"); - m->mothurOut("You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n"); - m->mothurOut("If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n"); - m->mothurOut("The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n"); - m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n"); - m->mothurOut("Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n"); - m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - int RemoveLineageCommand::execute(){ try { @@ -249,13 +275,40 @@ int RemoveLineageCommand::execute(){ if (listfile != "") { readList(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } if (outputNames.size() != 0) { 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(); + + //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("name"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } + } + + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + + itTypes = outputTypes.find("taxonomy"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); } + } } return 0; @@ -272,8 +325,7 @@ int RemoveLineageCommand::readFasta(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile); ofstream out; m->openOutputFile(outputFileName, out); @@ -284,7 +336,7 @@ int RemoveLineageCommand::readFasta(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } Sequence currSeq(in); name = currSeq.getName(); @@ -318,8 +370,7 @@ int RemoveLineageCommand::readList(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -338,7 +389,7 @@ int RemoveLineageCommand::readList(){ //for each bin for (int i = 0; i < list.getNumBins(); i++) { - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } //parse out names that are in accnos file string binnames = list.get(i); @@ -389,8 +440,7 @@ int RemoveLineageCommand::readName(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile); ofstream out; m->openOutputFile(outputFileName, out); @@ -401,22 +451,14 @@ int RemoveLineageCommand::readName(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> firstCol; in >> secondCol; vector parsedNames; - //parse second column saving each name - while (secondCol.find_first_of(',') != -1) { - name = secondCol.substr(0,secondCol.find_first_of(',')); - secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length()); - parsedNames.push_back(name); - } + m->splitAtComma(secondCol, parsedNames); - //get name after last , - parsedNames.push_back(secondCol); - vector validSecond; validSecond.clear(); for (int i = 0; i < parsedNames.size(); i++) { if (names.count(parsedNames[i]) == 0) { @@ -475,8 +517,7 @@ int RemoveLineageCommand::readGroup(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -487,7 +528,7 @@ int RemoveLineageCommand::readGroup(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> group; //read from second column @@ -518,7 +559,7 @@ int RemoveLineageCommand::readTax(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -528,120 +569,132 @@ int RemoveLineageCommand::readTax(){ bool wroteSomething = false; - bool taxonsHasConfidence = false; - vector< map > searchTaxons; - string noConfidenceTaxons = taxons; - int hasConPos = taxons.find_first_of('('); - if (hasConPos != string::npos) { - taxonsHasConfidence = true; - searchTaxons = getTaxons(taxons); - noConfidenceTaxons = removeConfidences(taxons); + vector taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false); + vector< vector< map > > searchTaxons; searchTaxons.resize(listOfTaxons.size()); + vector noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), ""); + + for (int i = 0; i < listOfTaxons.size(); i++) { + noConfidenceTaxons[i] = listOfTaxons[i]; + int hasConPos = listOfTaxons[i].find_first_of('('); + if (hasConPos != string::npos) { + taxonsHasConfidence[i] = true; + searchTaxons[i] = getTaxons(listOfTaxons[i]); + noConfidenceTaxons[i] = listOfTaxons[i]; + m->removeConfidences(noConfidenceTaxons[i]); + } } while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> tax; //read from second column - string newtax = tax; + bool remove = false; - //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them - if (!taxonsHasConfidence) { - - int hasConfidences = tax.find_first_of('('); - if (hasConfidences != string::npos) { - newtax = removeConfidences(tax); - } + for (int j = 0; j < listOfTaxons.size(); j++) { + string newtax = tax; - int pos = newtax.find(taxons); - - if (pos == string::npos) { - wroteSomething = true; - out << name << '\t' << tax << endl; - }else{ //this sequence contains the taxon the user wants to remove - names.insert(name); - } - - }else{//if taxons has them and you don't them remove taxons - int hasConfidences = tax.find_first_of('('); - if (hasConfidences == string::npos) { - - int pos = newtax.find(noConfidenceTaxons); + //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them + if (!taxonsHasConfidence[j]) { - if (pos == string::npos) { - wroteSomething = true; - out << name << '\t' << tax << endl; - }else{ //this sequence contains the taxon the user wants to remove - names.insert(name); - } - }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons - //first remove confidences from both and see if the taxonomy exists - - string noNewTax = tax; int hasConfidences = tax.find_first_of('('); if (hasConfidences != string::npos) { - noNewTax = removeConfidences(tax); + newtax = tax; + m->removeConfidences(newtax); } - int pos = noNewTax.find(noConfidenceTaxons); + int pos = newtax.find(noConfidenceTaxons[j]); - if (pos != string::npos) { //if yes, then are the confidences okay + if (pos == string::npos) { + //wroteSomething = true; + //out << name << '\t' << tax << endl; + }else{ //this sequence contains the taxon the user wants to remove + names.insert(name); + remove=true; break; + } + + }else{//if taxons has them and you don't them remove taxons + int hasConfidences = tax.find_first_of('('); + if (hasConfidences == string::npos) { + + int pos = newtax.find(noConfidenceTaxons[j]); + + if (pos == string::npos) { + //wroteSomething = true; + //out << name << '\t' << tax << endl; + }else{ //this sequence contains the taxon the user wants to remove + names.insert(name); + remove=true; break; + } + }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons + //first remove confidences from both and see if the taxonomy exists + + string noNewTax = tax; + int hasConfidences = tax.find_first_of('('); + if (hasConfidences != string::npos) { + noNewTax = tax; + m->removeConfidences(noNewTax); + } - bool remove = false; - vector< map > usersTaxon = getTaxons(newtax); + int pos = noNewTax.find(noConfidenceTaxons[j]); - //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4] - //we want to "line them up", so we will find the the index where the searchstring starts - int index = 0; - for (int i = 0; i < usersTaxon.size(); i++) { + if (pos != string::npos) { //if yes, then are the confidences okay - if (usersTaxon[i].begin()->first == searchTaxons[0].begin()->first) { - index = i; - int spot = 0; - bool goodspot = true; - //is this really the start, or are we dealing with a taxon of the same name? - while ((spot < searchTaxons.size()) && ((i+spot) < usersTaxon.size())) { - if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; } - else { spot++; } - } + vector< map > usersTaxon = getTaxons(newtax); + + //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4] + //we want to "line them up", so we will find the the index where the searchstring starts + int index = 0; + for (int i = 0; i < usersTaxon.size(); i++) { - if (goodspot) { break; } + if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) { + index = i; + int spot = 0; + bool goodspot = true; + //is this really the start, or are we dealing with a taxon of the same name? + while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) { + if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; } + else { spot++; } + } + + if (goodspot) { break; } + } } - } - - for (int i = 0; i < searchTaxons.size(); i++) { - if ((i+index) < usersTaxon.size()) { //just in case, should never be false - if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons + for (int i = 0; i < searchTaxons[j].size(); i++) { + + if ((i+index) < usersTaxon.size()) { //just in case, should never be false + if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons + remove = true; + break; + } + }else { remove = true; break; } + } + + //passed the test so remove you + if (remove) { + names.insert(name); + remove=true; break; }else { - remove = true; - break; + //wroteSomething = true; + //out << name << '\t' << tax << endl; } - } - - //passed the test so remove you - if (remove) { - names.insert(name); }else { - wroteSomething = true; - out << name << '\t' << tax << endl; + //wroteSomething = true; + //out << name << '\t' << tax << endl; } - }else { - wroteSomething = true; - out << name << '\t' << tax << endl; } } + } - - - + if (!remove) { wroteSomething = true; out << name << '\t' << tax << endl; } m->gobble(in); } in.close(); @@ -659,10 +712,10 @@ int RemoveLineageCommand::readTax(){ } } /**************************************************************************************************/ -vector< map > RemoveLineageCommand::getTaxons(string tax) { +vector< map > RemoveLineageCommand::getTaxons(string tax) { try { - vector< map > t; + vector< map > t; string taxon = ""; int taxLength = tax.length(); for(int i=0;i > RemoveLineageCommand::getTaxons(string tax) { newtaxon = taxon; confidence = "0"; } - int con = 0; + float con = 0; convert(confidence, con); - map temp; + map temp; temp[newtaxon] = con; t.push_back(temp); @@ -700,36 +753,13 @@ vector< map > RemoveLineageCommand::getTaxons(string tax) { exit(1); } } -/**************************************************************************************************/ -string RemoveLineageCommand::removeConfidences(string tax) { - try { - - string taxon = ""; - int taxLength = tax.length(); - for(int i=0;ierrorOut(e, "RemoveLineageCommand", "removeConfidences"); - exit(1); - } -} //********************************************************************************************************************** //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name int RemoveLineageCommand::readAlign(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report"; + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport"); ofstream out; m->openOutputFile(outputFileName, out); @@ -748,7 +778,7 @@ int RemoveLineageCommand::readAlign(){ out << endl; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column