X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removelineagecommand.cpp;h=7349203007d90b4228502680b95b93b7ab9c3240;hp=4cec90f567c764e8770987c150b67b5ececc0d35;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96 diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp index 4cec90f..7349203 100644 --- a/removelineagecommand.cpp +++ b/removelineagecommand.cpp @@ -10,20 +10,26 @@ #include "removelineagecommand.h" #include "sequence.hpp" #include "listvector.hpp" +#include "counttable.h" +#include "inputdata.h" //********************************************************************************************************************** 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); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT", "none","shared",false,false, true); parameters.push_back(pshared); + CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "tax", "FNGLT", "none","taxonomy",false,false, true); parameters.push_back(ptaxonomy); + CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "tax", "FNGLT", "none","constaxonomy",false,false, true); parameters.push_back(pconstaxonomy); + CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter ptaxon("taxon", "String", "", "", "", "", "","",false,true,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); } @@ -38,13 +44,14 @@ vector RemoveLineageCommand::setParameters(){ 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 remove.lineage command reads a taxonomy or constaxonomy file and any of the following file types: fasta, name, group, count, list, shared or alignreport file. The constaxonomy can only be used with a shared or list file.\n"; + helpString += "It outputs a file containing only the sequences or OTUS 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, count, list, shared, taxonomy, alignreport, label and dups. You must provide taxonomy or constaxonomy 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 label parameter is used to analyze specific labels in your input. \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"; @@ -58,30 +65,29 @@ string RemoveLineageCommand::getHelpString(){ } } //********************************************************************************************************************** -string RemoveLineageCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string RemoveLineageCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //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", "getOutputFileNameTag"); - exit(1); - } + if (type == "fasta") { pattern = "[filename],pick,[extension]"; } + else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; } + else if (type == "constaxonomy") { pattern = "[filename],pick,[extension]"; } + else if (type == "name") { pattern = "[filename],pick,[extension]"; } + else if (type == "group") { pattern = "[filename],pick,[extension]"; } + else if (type == "count") { pattern = "[filename],pick,[extension]"; } + else if (type == "list") { pattern = "[filename],[distance],pick,[extension]"; } + else if (type == "shared") { pattern = "[filename],[distance],pick,[extension]"; } + else if (type == "alignreport") { pattern = "[filename],pick.align.report"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "RemoveLineageCommand", "getOutputPattern"); + exit(1); + } } + //********************************************************************************************************************** RemoveLineageCommand::RemoveLineageCommand(){ try { @@ -94,6 +100,10 @@ RemoveLineageCommand::RemoveLineageCommand(){ outputTypes["group"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; outputTypes["list"] = tempOutNames; + outputTypes["count"] = tempOutNames; + outputTypes["constaxonomy"] = tempOutNames; + outputTypes["shared"] = tempOutNames; + } catch(exception& e) { m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand"); @@ -131,6 +141,10 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { outputTypes["group"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; outputTypes["list"] = tempOutNames; + outputTypes["count"] = tempOutNames; + outputTypes["constaxonomy"] = tempOutNames; + outputTypes["shared"] = 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 = ""; } @@ -187,6 +201,30 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["taxonomy"] = inputDir + it->second; } } + + it = parameters.find("count"); + //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["count"] = inputDir + it->second; } + } + + it = parameters.find("constaxonomy"); + //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["constaxonomy"] = inputDir + it->second; } + } + + it = parameters.find("shared"); + //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["shared"] = inputDir + it->second; } + } } @@ -217,12 +255,40 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { 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); } + else if (taxfile == "not found") { taxfile = ""; } + else { m->setTaxonomyFile(taxfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { m->setSharedFile(sharedfile); } + + + constaxonomy = validParameter.validFile(parameters, "constaxonomy", true); + if (constaxonomy == "not open") { constaxonomy = ""; abort = true; } + else if (constaxonomy == "not found") { constaxonomy = ""; } + + if ((constaxonomy == "") && (taxfile == "")) { + 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 did not provide a constaxonomy file. The taxonomy or constaxonomy parameter is required."); m->mothurOutEndLine(); abort = true; } + } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { countfile = ""; abort = true; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((namefile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true; + } + + if ((groupfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true; + } + string usedDups = "true"; string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { @@ -240,14 +306,34 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { } 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 ((fastafile == "") && (constaxonomy == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy, constaxonomy, shared or listfile."); m->mothurOutEndLine(); abort = true; } + + if ((constaxonomy != "") && ((fastafile != "") || (namefile != "") || (groupfile != "") || (alignfile != "") || (taxfile != "") || (countfile != ""))) { + m->mothurOut("[ERROR]: can only use constaxonomy file with a list or shared file, aborting.\n"); abort = true; + } + + if ((constaxonomy != "") && (taxfile != "")) { + m->mothurOut("[ERROR]: Choose only one: taxonomy or constaxonomy, aborting.\n"); abort = true; + } + + if ((sharedfile != "") && (taxfile != "")) { + m->mothurOut("[ERROR]: sharedfile can only be used with constaxonomy file, aborting.\n"); abort = true; + } + + if ((sharedfile != "") || (listfile != "")) { + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; } + } + 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); - } + if (countfile == "") { + if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } + } } @@ -265,14 +351,28 @@ int RemoveLineageCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } if (m->control_pressed) { return 0; } + + if (countfile != "") { + if ((fastafile != "") || (listfile != "") || (taxfile != "")) { + m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n"); + } + } //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 (taxfile != "") { + readTax(); //fills the set of names to get + if (namefile != "") { readName(); } + if (fastafile != "") { readFasta(); } + if (countfile != "") { readCount(); } + if (groupfile != "") { readGroup(); } + if (alignfile != "") { readAlign(); } + if (listfile != "") { readList(); } + + }else { + readConsTax(); + if (listfile != "") { readConsList(); } + if (sharedfile != "") { readShared(); } + } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -309,6 +409,11 @@ int RemoveLineageCommand::execute(){ if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); } } + + itTypes = outputTypes.find("count"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); } + } } return 0; @@ -325,7 +430,10 @@ int RemoveLineageCommand::readFasta(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)); + variables["[extension]"] = m->getExtension(fastafile); + string outputFileName = getOutputFileName("fasta", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -370,9 +478,9 @@ int RemoveLineageCommand::readList(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile); - ofstream out; - m->openOutputFile(outputFileName, out); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[extension]"] = m->getExtension(listfile); ifstream in; m->openInputFile(listfile, in); @@ -380,12 +488,25 @@ int RemoveLineageCommand::readList(){ bool wroteSomething = false; while(!in.eof()){ + //read in list vector ListVector list(in); //make a new list vector ListVector newList; newList.setLabel(list.getLabel()); + + variables["[distance]"] = list.getLabel(); + string outputFileName = getOutputFileName("list", variables); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName); + + if (m->control_pressed) { in.close(); out.close(); return 0; } + + vector binLabels = list.getLabels(); + vector newBinLabels; //for each bin for (int i = 0; i < list.getNumBins(); i++) { @@ -393,39 +514,39 @@ int RemoveLineageCommand::readList(){ //parse out names that are in accnos file string binnames = list.get(i); + vector bnames; + m->splitAtComma(binnames, bnames); 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()); - + for (int j = 0; j < bnames.size(); j++) { + string name = bnames[j]; //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); + newList.push_back(newNames); + newBinLabels.push_back(binLabels[i]); } } //print new listvector if (newList.getNumBins() != 0) { wroteSomething = true; + newList.setLabels(newBinLabels); + newList.printHeaders(out); newList.print(out); } m->gobble(in); + out.close(); } 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; @@ -440,7 +561,10 @@ int RemoveLineageCommand::readName(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile)); + variables["[extension]"] = m->getExtension(namefile); + string outputFileName = getOutputFileName("name", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -511,13 +635,364 @@ int RemoveLineageCommand::readName(){ exit(1); } } +//********************************************************************************************************************** +int RemoveLineageCommand::readCount(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(countfile); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile)); + variables["[extension]"] = m->getExtension(countfile); + string outputFileName = getOutputFileName("count", variables); + + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(countfile, in); + + bool wroteSomething = false; + + string headers = m->getline(in); m->gobble(in); + out << headers << endl; + + string name, rest; int thisTotal; + while (!in.eof()) { + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; m->gobble(in); + in >> thisTotal; m->gobble(in); + rest = m->getline(in); m->gobble(in); + if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); } + + if (names.count(name) == 0) { + out << name << '\t' << thisTotal << '\t' << rest << endl; + wroteSomething = true; + } + } + in.close(); + out.close(); + + //check for groups that have been eliminated + CountTable ct; + if (ct.testGroups(outputFileName)) { + ct.readTable(outputFileName, true, false); + ct.printTable(outputFileName); + } + + if (wroteSomething == false) { m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); } + outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "RemoveLineageCommand", "readCount"); + exit(1); + } +} +//********************************************************************************************************************** +int RemoveLineageCommand::readConsList(){ + try { + getListVector(); + + if (m->control_pressed) { delete list; return 0;} + + ListVector newList; + newList.setLabel(list->getLabel()); + int removedCount = 0; + bool wroteSomething = false; + string snumBins = toString(list->getNumBins()); + + vector binLabels = list->getLabels(); + vector newBinLabels; + for (int i = 0; i < list->getNumBins(); i++) { + + if (m->control_pressed) { delete list; return 0;} + + //create a label for this otu + string otuLabel = "Otu"; + string sbinNumber = toString(i+1); + if (sbinNumber.length() < snumBins.length()) { + int diff = snumBins.length() - sbinNumber.length(); + for (int h = 0; h < diff; h++) { otuLabel += "0"; } + } + otuLabel += sbinNumber; + + if (names.count(m->getSimpleLabel(otuLabel)) == 0) { + newList.push_back(list->get(i)); + newBinLabels.push_back(binLabels[i]); + }else { removedCount++; } + } + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[extension]"] = m->getExtension(listfile); + variables["[distance]"] = list->getLabel(); + string outputFileName = getOutputFileName("list", variables); + ofstream out; + m->openOutputFile(outputFileName, out); + + delete list; + //print new listvector + if (newList.getNumBins() != 0) { + wroteSomething = true; + newList.setLabels(newBinLabels); + newList.printHeaders(out); + newList.print(out); + } + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file only contains OTUs from " + taxons + "."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName); + + m->mothurOut("Removed " + toString(removedCount) + " OTUs from your list file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "RemoveLineageCommand", "readConsList"); + exit(1); + } +} +//********************************************************************************************************************** +int RemoveLineageCommand::getListVector(){ + try { + InputData input(listfile, "list"); + list = input.getListVector(); + string lastLabel = list->getLabel(); + + if (label == "") { label = lastLabel; return 0; } + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set labels; labels.insert(label); + set processedLabels; + set userLabels = labels; + + //as long as you are not at the end of the file or done wih the lines you want + while((list != NULL) && (userLabels.size() != 0)) { + if (m->control_pressed) { return 0; } + + if(labels.count(list->getLabel()) == 1){ + processedLabels.insert(list->getLabel()); + userLabels.erase(list->getLabel()); + break; + } + + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = list->getLabel(); + + delete list; + list = input.getListVector(lastLabel); + + processedLabels.insert(list->getLabel()); + userLabels.erase(list->getLabel()); + + //restore real lastlabel to save below + list->setLabel(saveLabel); + break; + } + + lastLabel = list->getLabel(); + + //get next line to process + //prevent memory leak + delete list; + list = input.getListVector(); + } + + + if (m->control_pressed) { return 0; } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; + }else { + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + } + } + + //run last label if you need to + if (needToRun == true) { + delete list; + list = input.getListVector(lastLabel); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "RemoveLineageCommand", "getListVector"); + exit(1); + } +} + +//********************************************************************************************************************** +int RemoveLineageCommand::readShared(){ + try { + + getShared(); + + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } + + vector newLabels; + + //create new "filtered" lookup + vector newLookup; + for (int i = 0; i < lookup.size(); i++) { + SharedRAbundVector* temp = new SharedRAbundVector(); + temp->setLabel(lookup[i]->getLabel()); + temp->setGroup(lookup[i]->getGroup()); + newLookup.push_back(temp); + } + + bool wroteSomething = false; + int numRemoved = 0; + for (int i = 0; i < lookup[0]->getNumBins(); i++) { + + if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; } + + //is this otu on the list + if (names.count(m->getSimpleLabel(m->currentSharedBinLabels[i])) == 0) { + wroteSomething = true; + newLabels.push_back(m->currentSharedBinLabels[i]); + for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup + newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup()); + } + }else { numRemoved++; } + } + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[extension]"] = m->getExtension(sharedfile); + variables["[distance]"] = lookup[0]->getLabel(); + string outputFileName = getOutputFileName("shared", variables); + ofstream out; + m->openOutputFile(outputFileName, out); + outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName); + + for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } + + m->currentSharedBinLabels = newLabels; + + newLookup[0]->printHeaders(out); + + for (int i = 0; i < newLookup.size(); i++) { + out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t'; + newLookup[i]->print(out); + } + out.close(); + + for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } + + if (wroteSomething == false) { m->mothurOut("Your file only contains OTUs from " + taxons + "."); m->mothurOutEndLine(); } + + m->mothurOut("Removed " + toString(numRemoved) + " OTUs from your shared file."); m->mothurOutEndLine(); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "RemoveLineageCommand", "readShared"); + exit(1); + } +} +//********************************************************************************************************************** +int RemoveLineageCommand::getShared(){ + try { + InputData input(sharedfile, "sharedfile"); + lookup = input.getSharedRAbundVectors(); + string lastLabel = lookup[0]->getLabel(); + + if (label == "") { label = lastLabel; return 0; } + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set labels; labels.insert(label); + set processedLabels; + set userLabels = labels; + + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && (userLabels.size() != 0)) { + if (m->control_pressed) { return 0; } + + if(labels.count(lookup[0]->getLabel()) == 1){ + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + break; + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundVectors(lastLabel); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + break; + } + + lastLabel = lookup[0]->getLabel(); + + //get next line to process + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundVectors(); + } + + + if (m->control_pressed) { return 0; } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; + }else { + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + } + } + + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input.getSharedRAbundVectors(lastLabel); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "RemoveLineageCommand", "getShared"); + exit(1); + } +} + //********************************************************************************************************************** int RemoveLineageCommand::readGroup(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)); + variables["[extension]"] = m->getExtension(groupfile); + string outputFileName = getOutputFileName("group", variables); + ofstream out; m->openOutputFile(outputFileName, out); @@ -559,7 +1034,10 @@ int RemoveLineageCommand::readTax(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)); + variables["[extension]"] = m->getExtension(taxfile); + string outputFileName = getOutputFileName("taxonomy", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -594,15 +1072,17 @@ int RemoveLineageCommand::readTax(){ bool remove = false; + string noQuotesTax = m->removeQuotes(tax); + for (int j = 0; j < listOfTaxons.size(); j++) { - string newtax = tax; + string newtax = noQuotesTax; //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('('); + int hasConfidences = noQuotesTax.find_first_of('('); if (hasConfidences != string::npos) { - newtax = tax; + newtax = noQuotesTax; m->removeConfidences(newtax); } @@ -617,7 +1097,7 @@ int RemoveLineageCommand::readTax(){ } }else{//if taxons has them and you don't them remove taxons - int hasConfidences = tax.find_first_of('('); + int hasConfidences = noQuotesTax.find_first_of('('); if (hasConfidences == string::npos) { int pos = newtax.find(noConfidenceTaxons[j]); @@ -632,10 +1112,10 @@ int RemoveLineageCommand::readTax(){ }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('('); + string noNewTax = noQuotesTax; + int hasConfidences = noQuotesTax.find_first_of('('); if (hasConfidences != string::npos) { - noNewTax = tax; + noNewTax = noQuotesTax; m->removeConfidences(noNewTax); } @@ -711,6 +1191,174 @@ int RemoveLineageCommand::readTax(){ exit(1); } } +//********************************************************************************************************************** +int RemoveLineageCommand::readConsTax(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomy); } + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomy)); + variables["[extension]"] = m->getExtension(constaxonomy); + string outputFileName = getOutputFileName("constaxonomy", variables); + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(constaxonomy, in); + string otuLabel, tax; + int numReps; + bool wroteSomething = false; + + //read headers + string headers = m->getline(in); + out << headers << endl; + + //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 >> otuLabel; m->gobble(in); + in >> numReps; m->gobble(in); + in >> tax; m->gobble(in); + + bool remove = false; + + string noQuotesTax = m->removeQuotes(tax); + + for (int j = 0; j < listOfTaxons.size(); j++) { + string newtax = noQuotesTax; + + //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 = noQuotesTax.find_first_of('('); + if (hasConfidences != string::npos) { + newtax = noQuotesTax; + 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(m->getSimpleLabel(otuLabel)); + remove=true; break; + } + + }else{//if taxons has them and you don't them remove taxons + int hasConfidences = noQuotesTax.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(m->getSimpleLabel(otuLabel)); + 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 = noQuotesTax; + int hasConfidences = noQuotesTax.find_first_of('('); + if (hasConfidences != string::npos) { + noNewTax = noQuotesTax; + 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(m->getSimpleLabel(otuLabel)); + remove=true; break; + }else { + //wroteSomething = true; + //out << name << '\t' << tax << endl; + } + }else { + //wroteSomething = true; + //out << name << '\t' << tax << endl; + } + } + } + + } + + if (!remove) { wroteSomething = true; out << otuLabel << '\t' << numReps << '\t' << tax << endl; } + + } + in.close(); + out.close(); + + if (names.size() == 0) { m->mothurOut("Your constaxonomy file contains OTUs only from " + taxons + "."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "RemoveLineageCommand", "readConsTax"); + exit(1); + } +} /**************************************************************************************************/ vector< map > RemoveLineageCommand::getTaxons(string tax) { try { @@ -720,25 +1368,30 @@ vector< map > RemoveLineageCommand::getTaxons(string tax) { int taxLength = tax.length(); for(int i=0;iisNumeric1(confidenceScore)) { //its a confidence + newtaxon = taxon.substr(0, openParen); //rip off confidence + confidence = taxon.substr((openParen+1), (closeParen-openParen-1)); + }else { //its part of the taxon + newtaxon = taxon; + confidence = "0"; + } }else{ newtaxon = taxon; confidence = "0"; - } + } float con = 0; convert(confidence, con); map temp; temp[newtaxon] = con; t.push_back(temp); - taxon = ""; } else{ @@ -759,7 +1412,10 @@ int RemoveLineageCommand::readAlign(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport"); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)); + variables["[extension]"] = m->getExtension(alignfile); + string outputFileName = getOutputFileName("alignreport", variables); ofstream out; m->openOutputFile(outputFileName, out);