X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.cpp;fp=getlineagecommand.cpp;h=1cd139b5213733e759a7a32a1fbdf8221d09dfb6;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=1aba0fed4e6e772de07718a544335b6e6bb58db9;hpb=159fd324dfecacb6617669246d85c787ae67f630;p=mothur.git diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp index 1aba0fe..1cd139b 100644 --- a/getlineagecommand.cpp +++ b/getlineagecommand.cpp @@ -15,8 +15,9 @@ vector GetLineageCommand::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 pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "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); @@ -38,9 +39,9 @@ vector GetLineageCommand::setParameters(){ string GetLineageCommand::getHelpString(){ try { string helpString = ""; - helpString += "The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n"; + helpString += "The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, count, list or alignreport file.\n"; helpString += "It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n"; - helpString += "The get.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 get.lineage command parameters are taxon, fasta, name, group, count, 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 get and is required.\n"; helpString += "You may enter your taxons with confidence scores, doing so will get only those sequences that belong to the taxonomy and whose cofidence scores is above the scores you give.\n"; @@ -70,6 +71,7 @@ string GetLineageCommand::getOutputFileNameTag(string type, string inputName="") 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 == "count") { outputFileName = "pick.count.table"; } 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"; } @@ -94,6 +96,7 @@ GetLineageCommand::GetLineageCommand(){ outputTypes["group"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; outputTypes["list"] = tempOutNames; + outputTypes["count"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "GetLineageCommand", "GetLineageCommand"); @@ -131,6 +134,7 @@ GetLineageCommand::GetLineageCommand(string option) { outputTypes["group"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; outputTypes["list"] = tempOutNames; + outputTypes["count"] = 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 +191,14 @@ GetLineageCommand::GetLineageCommand(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; } + } } @@ -230,6 +242,19 @@ GetLineageCommand::GetLineageCommand(string option) { else { temp = "false"; usedDups = ""; } } dups = m->isTrue(temp); + + 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; + } taxons = validParameter.validFile(parameters, "taxon", false); if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; } @@ -240,12 +265,14 @@ GetLineageCommand::GetLineageCommand(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 == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, count, 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); - } + if (countfile == "") { + if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } + } } } @@ -262,11 +289,18 @@ int GetLineageCommand::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 get if (namefile != "") { readName(); } if (fastafile != "") { readFasta(); } + if (countfile != "") { readCount(); } if (groupfile != "") { readGroup(); } if (alignfile != "") { readAlign(); } if (listfile != "") { readList(); } @@ -305,7 +339,12 @@ int GetLineageCommand::execute(){ itTypes = outputTypes.find("taxonomy"); 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; @@ -353,7 +392,7 @@ int GetLineageCommand::readFasta(){ in.close(); out.close(); - if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); } outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); return 0; @@ -365,6 +404,52 @@ int GetLineageCommand::readFasta(){ } } //********************************************************************************************************************** +int GetLineageCommand::readCount(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(countfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile); + + 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(); + + if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); } + outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "GetLineageCommand", "readCount"); + exit(1); + } +} +//********************************************************************************************************************** int GetLineageCommand::readList(){ try { string thisOutputDir = outputDir; @@ -425,7 +510,7 @@ int GetLineageCommand::readList(){ in.close(); out.close(); - if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); } outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName); return 0; @@ -510,7 +595,7 @@ int GetLineageCommand::readName(){ in.close(); out.close(); - if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); } outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName); return 0; @@ -558,7 +643,7 @@ int GetLineageCommand::readGroup(){ in.close(); out.close(); - if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); } outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName); return 0; @@ -814,7 +899,7 @@ int GetLineageCommand::readAlign(){ in.close(); out.close(); - if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); } outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName); return 0;