X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.cpp;h=1aba0fed4e6e772de07718a544335b6e6bb58db9;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=dd00c0368c3e8167f26667d40af1925f184feb32;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp index dd00c03..1aba0fe 100644 --- a/getlineagecommand.cpp +++ b/getlineagecommand.cpp @@ -57,7 +57,31 @@ string GetLineageCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string GetLineageCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + 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, "GetLineageCommand", "getOutputFileNameTag"); + exit(1); + } +} //********************************************************************************************************************** GetLineageCommand::GetLineageCommand(){ try { @@ -83,6 +107,7 @@ GetLineageCommand::GetLineageCommand(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 { vector myArray = setParameters(); @@ -167,16 +192,19 @@ GetLineageCommand::GetLineageCommand(string option) { //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; } + 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; } @@ -185,14 +213,15 @@ GetLineageCommand::GetLineageCommand(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; } + 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); @@ -209,9 +238,14 @@ GetLineageCommand::GetLineageCommand(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 ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } } } @@ -238,7 +272,7 @@ int GetLineageCommand::execute(){ if (listfile != "") { readList(); } - if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } if (outputNames.size() != 0) { m->mothurOutEndLine(); @@ -288,7 +322,7 @@ int GetLineageCommand::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); @@ -301,7 +335,7 @@ int GetLineageCommand::readFasta(){ 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(); @@ -335,7 +369,7 @@ int GetLineageCommand::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); @@ -346,7 +380,7 @@ int GetLineageCommand::readList(){ 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; } //read in list vector ListVector list(in); @@ -407,7 +441,7 @@ int GetLineageCommand::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); @@ -421,7 +455,7 @@ int GetLineageCommand::readName(){ 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; @@ -493,7 +527,7 @@ int GetLineageCommand::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); @@ -506,7 +540,7 @@ int GetLineageCommand::readGroup(){ 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 @@ -540,7 +574,7 @@ int GetLineageCommand::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); @@ -549,110 +583,121 @@ int GetLineageCommand::readTax(){ string name, tax; //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; - + 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) { - int hasConfidences = tax.find_first_of('('); - if (hasConfidences != string::npos) { - newtax = removeConfidences(tax); - } - - int pos = newtax.find(taxons); + //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); + } - if (pos != string::npos) { //this sequence contains the taxon the user wants - names.insert(name); - out << name << '\t' << tax << endl; - } + int pos = newtax.find(noConfidenceTaxons[j]); - }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 (pos != string::npos) { //this sequence contains the taxon the user wants - names.insert(name); + names.insert(name); out << name << '\t' << tax << endl; + //since you belong to at least one of the taxons we want you are included so no need to search for other + 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; + }else{//if listOfTaxons[i] has them and you don't them remove taxons int hasConfidences = tax.find_first_of('('); - if (hasConfidences != string::npos) { - noNewTax = removeConfidences(tax); - } + if (hasConfidences == string::npos) { + + int pos = newtax.find(noConfidenceTaxons[j]); + + if (pos != string::npos) { //this sequence contains the taxon the user wants + names.insert(name); + out << name << '\t' << tax << endl; + //since you belong to at least one of the taxons we want you are included so no need to search for other + 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 - int pos = noNewTax.find(noConfidenceTaxons); + 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 + if (pos != string::npos) { //if yes, then are the confidences okay - bool good = true; - vector< map > usersTaxon = getTaxons(newtax); + bool good = true; + 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++) { + //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[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++; } - } + 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; } + if (goodspot) { break; } + } } - } - for (int i = 0; i < searchTaxons.size(); i++) { + 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[i].begin()->second) { //is the users cutoff less than the search taxons + 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 + good = false; + break; + } + }else { good = false; break; } - }else { - good = false; - break; } - } - //passed the test so add you - if (good) { - names.insert(name); - out << name << '\t' << tax << endl; + //passed the test so add you + if (good) { + names.insert(name); + out << name << '\t' << tax << endl; + break; + } } } } - } - + } m->gobble(in); } @@ -712,36 +757,13 @@ vector< map > GetLineageCommand::getTaxons(string tax) { exit(1); } } -/**************************************************************************************************/ -string GetLineageCommand::removeConfidences(string tax) { - try { - - string taxon = ""; - int taxLength = tax.length(); - for(int i=0;ierrorOut(e, "GetLineageCommand", "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 GetLineageCommand::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); @@ -761,7 +783,7 @@ int GetLineageCommand::readAlign(){ 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