X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;fp=removelineagecommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=9fec2496068950b4863448fe500b17cbc957670a;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp deleted file mode 100644 index 9fec249..0000000 --- a/removelineagecommand.cpp +++ /dev/null @@ -1,805 +0,0 @@ -/* - * removelineagecommand.cpp - * Mothur - * - * Created by westcott on 9/24/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "removelineagecommand.h" -#include "sequence.hpp" -#include "listvector.hpp" - -//********************************************************************************************************************** -vector RemoveLineageCommand::setParameters(){ - try { - 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", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string RemoveLineageCommand::getHelpString(){ - try { - 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", "getHelpString"); - exit(1); - } -} - - -//********************************************************************************************************************** -RemoveLineageCommand::RemoveLineageCommand(){ - try { - 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", "RemoveLineageCommand"); - exit(1); - } -} -//********************************************************************************************************************** -RemoveLineageCommand::RemoveLineageCommand(string option) { - try { - abort = false; calledHelp = false; - - //allow user to run help - if(option == "help") { help(); abort = true; calledHelp = true; } - else if(option == "citation") { citation(); abort = true; calledHelp = true;} - - else { - vector myArray = setParameters(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - map::iterator it; - - //check to make sure all parameters are valid for command - for (it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - //initialize outputTypes - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["taxonomy"] = tempOutNames; - outputTypes["name"] = tempOutNames; - outputTypes["group"] = tempOutNames; - outputTypes["alignreport"] = tempOutNames; - outputTypes["list"] = tempOutNames; - - //if the user changes the output directory command factory will send this info to us in the output parameter - outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } - - //if the user changes the input directory command factory will send this info to us in the output parameter - string inputDir = validParameter.validFile(parameters, "inputdir", false); - if (inputDir == "not found"){ inputDir = ""; } - else { - string path; - it = parameters.find("alignreport"); - //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["alignreport"] = inputDir + it->second; } - } - - 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["fasta"] = inputDir + it->second; } - } - - it = parameters.find("list"); - //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["list"] = inputDir + it->second; } - } - - it = parameters.find("name"); - //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["name"] = inputDir + it->second; } - } - - it = parameters.find("group"); - //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["group"] = inputDir + it->second; } - } - - it = parameters.find("taxonomy"); - //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["taxonomy"] = inputDir + it->second; } - } - } - - - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", 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") { 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; } - else if (alignfile == "not found") { alignfile = ""; } - - 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") { 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); - if (temp == "not found") { - if (namefile != "") { temp = "true"; } - else { temp = "false"; usedDups = ""; } - } - dups = m->isTrue(temp); - - taxons = validParameter.validFile(parameters, "taxon", false); - if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; } - else { - //rip off quotes - 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); - } - - } - - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -int RemoveLineageCommand::execute(){ - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - if (m->control_pressed) { return 0; } - - //read through the correct file and output lines you want to keep - if (taxfile != "") { readTax(); } //fills the set of names to remove - if (namefile != "") { readName(); } - if (fastafile != "") { readFasta(); } - if (groupfile != "") { readGroup(); } - if (alignfile != "") { readAlign(); } - if (listfile != "") { readList(); } - - - 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; - } - - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "execute"); - exit(1); - } -} - -//********************************************************************************************************************** -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); - - ofstream out; - m->openOutputFile(outputFileName, out); - - ifstream in; - m->openInputFile(fastafile, in); - string name; - - bool wroteSomething = false; - - while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } - - Sequence currSeq(in); - name = currSeq.getName(); - - if (name != "") { - //if this name is in the accnos file - if (names.count(name) == 0) { - wroteSomething = true; - - currSeq.printSequence(out); - } - } - m->gobble(in); - } - in.close(); - out.close(); - - if (wroteSomething == false) { m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "readFasta"); - exit(1); - } -} -//********************************************************************************************************************** -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); - - ofstream out; - m->openOutputFile(outputFileName, out); - - ifstream in; - m->openInputFile(listfile, in); - - bool wroteSomething = false; - - while(!in.eof()){ - //read in list vector - ListVector list(in); - - //make a new list vector - ListVector newList; - newList.setLabel(list.getLabel()); - - //for each bin - for (int i = 0; i < list.getNumBins(); i++) { - 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); - - string newNames = ""; - while (binnames.find_first_of(',') != -1) { - string name = binnames.substr(0,binnames.find_first_of(',')); - binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length()); - - //if that name is in the .accnos file, add it - if (names.count(name) == 0) { newNames += name + ","; } - } - - //get last name - if (names.count(binnames) == 0) { newNames += binnames + ","; } - - //if there are names in this bin add to new list - if (newNames != "") { - newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma - newList.push_back(newNames); - } - } - - //print new listvector - if (newList.getNumBins() != 0) { - wroteSomething = true; - newList.print(out); - } - - m->gobble(in); - } - in.close(); - out.close(); - - if (wroteSomething == false) { m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName); - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "readList"); - exit(1); - } -} -//********************************************************************************************************************** -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); - - ofstream out; - m->openOutputFile(outputFileName, out); - - ifstream in; - m->openInputFile(namefile, in); - string name, firstCol, secondCol; - - bool wroteSomething = false; - - while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } - - in >> firstCol; - in >> secondCol; - - vector parsedNames; - m->splitAtComma(secondCol, parsedNames); - - vector validSecond; validSecond.clear(); - for (int i = 0; i < parsedNames.size(); i++) { - if (names.count(parsedNames[i]) == 0) { - validSecond.push_back(parsedNames[i]); - } - } - - if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone - for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); } - }else { - //if the name in the first column is in the set then print it and any other names in second column also in set - if (names.count(firstCol) == 0) { - - wroteSomething = true; - - out << firstCol << '\t'; - - //you know you have at least one valid second since first column is valid - for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } - out << validSecond[validSecond.size()-1] << endl; - - //make first name in set you come to first column and then add the remaining names to second column - }else { - - //you want part of this row - if (validSecond.size() != 0) { - - wroteSomething = true; - - out << validSecond[0] << '\t'; - - //you know you have at least one valid second since first column is valid - for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } - out << validSecond[validSecond.size()-1] << endl; - } - } - } - m->gobble(in); - } - in.close(); - out.close(); - - if (wroteSomething == false) { m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName); - - return 0; - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "readName"); - exit(1); - } -} - -//********************************************************************************************************************** -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); - - ofstream out; - m->openOutputFile(outputFileName, out); - - ifstream in; - m->openInputFile(groupfile, in); - string name, group; - - bool wroteSomething = false; - - while(!in.eof()){ - 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 - - //if this name is in the accnos file - if (names.count(name) == 0) { - wroteSomething = true; - out << name << '\t' << group << endl; - } - - m->gobble(in); - } - in.close(); - out.close(); - - if (wroteSomething == false) { m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName); - - return 0; - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "readGroup"); - exit(1); - } -} -//********************************************************************************************************************** -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); - ofstream out; - m->openOutputFile(outputFileName, out); - - ifstream in; - m->openInputFile(taxfile, in); - string name, tax; - - bool wroteSomething = false; - - 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(); m->mothurRemove(outputFileName); return 0; } - - in >> name; //read from first column - in >> tax; //read from second column - - bool remove = false; - - for (int j = 0; j < listOfTaxons.size(); j++) { - string newtax = tax; - - //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]) { - - int hasConfidences = tax.find_first_of('('); - if (hasConfidences != string::npos) { - newtax = tax; - m->removeConfidences(newtax); - } - - 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{//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); - } - - int pos = noNewTax.find(noConfidenceTaxons[j]); - - if (pos != string::npos) { //if yes, then are the confidences okay - - 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 (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[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 { - //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(); - out.close(); - - if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName); - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "readTax"); - exit(1); - } -} -/**************************************************************************************************/ -vector< map > RemoveLineageCommand::getTaxons(string tax) { - try { - - vector< map > t; - string taxon = ""; - int taxLength = tax.length(); - for(int i=0;i temp; - temp[newtaxon] = con; - t.push_back(temp); - - taxon = ""; - } - else{ - taxon += tax[i]; - } - } - - return t; - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "getTaxons"); - 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"; - - ofstream out; - m->openOutputFile(outputFileName, out); - - ifstream in; - m->openInputFile(alignfile, in); - string name, junk; - - bool wroteSomething = false; - - //read column headers - for (int i = 0; i < 16; i++) { - if (!in.eof()) { in >> junk; out << junk << '\t'; } - else { break; } - } - out << endl; - - while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } - - in >> name; //read from first column - - //if this name is in the accnos file - if (names.count(name) == 0) { - wroteSomething = true; - - out << name << '\t'; - - //read rest - for (int i = 0; i < 15; i++) { - if (!in.eof()) { in >> junk; out << junk << '\t'; } - else { break; } - } - out << endl; - - }else {//still read just don't do anything with it - - //read rest - for (int i = 0; i < 15; i++) { - if (!in.eof()) { in >> junk; } - else { break; } - } - } - - m->gobble(in); - } - in.close(); - out.close(); - - if (wroteSomething == false) { m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName); - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "RemoveLineageCommand", "readAlign"); - exit(1); - } -} -//********************************************************************************************************************** -