X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=phylotypecommand.cpp;h=b21865abb54472b29473a76e2a9898939f7904c5;hp=c03fcc1ac133572fc7d821816edadc0b1fc32ecb;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77 diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp index c03fcc1..b21865a 100644 --- a/phylotypecommand.cpp +++ b/phylotypecommand.cpp @@ -16,12 +16,13 @@ //********************************************************************************************************************** vector PhylotypeCommand::setParameters(){ try { - CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); - CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pcutoff); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + 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); } @@ -37,7 +38,7 @@ string PhylotypeCommand::getHelpString(){ try { string helpString = ""; helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n"; - helpString += "The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n"; + helpString += "The phylotype command parameter options are taxonomy, name, count, cutoff and label. The taxonomy parameter is required.\n"; helpString += "The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n"; helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n"; helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n"; @@ -53,7 +54,23 @@ string PhylotypeCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string PhylotypeCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; } + else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; } + else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "PhylotypeCommand", "getOutputPattern"); + exit(1); + } +} //********************************************************************************************************************** PhylotypeCommand::PhylotypeCommand(){ try { @@ -118,6 +135,14 @@ PhylotypeCommand::PhylotypeCommand(string option) { //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("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; } + } } taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true); @@ -128,12 +153,18 @@ PhylotypeCommand::PhylotypeCommand(string option) { m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine(); abort = true; } - }else if (taxonomyFileName == "not open") { abort = true; } + }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; } + else { m->setTaxonomyFile(taxonomyFileName); } 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 { readNamesFile(); } + else { readNamesFile(); m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } //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"){ @@ -141,9 +172,11 @@ PhylotypeCommand::PhylotypeCommand(string option) { outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it } + if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } + string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "-1"; } - convert(temp, cutoff); + m->mothurConvert(temp, cutoff); label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; allLines = 1; } @@ -152,6 +185,12 @@ PhylotypeCommand::PhylotypeCommand(string option) { else { allLines = 1; } } + if (countfile == "") { + if (namefile == "") { + vector files; files.push_back(taxonomyFileName); + parser.getNameFile(files); + } + } } } catch(exception& e) { @@ -189,22 +228,27 @@ int PhylotypeCommand::execute(){ if (m->control_pressed) { delete tree; return 0; } - string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName)); - - ofstream outList; - string outputListFile = fileroot + "tx.list"; - m->openOutputFile(outputListFile, outList); - ofstream outSabund; - string outputSabundFile = fileroot + "tx.sabund"; - m->openOutputFile(outputSabundFile, outSabund); - ofstream outRabund; - string outputRabundFile = fileroot + "tx.rabund"; - m->openOutputFile(outputRabundFile, outRabund); - - outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile); - outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile); - outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile); - + ofstream outList, outRabund, outSabund; + map variables; + string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName)); + variables["[filename]"] = fileroot; + variables["[clustertag]"] = "tx"; + string sabundFileName = getOutputFileName("sabund", variables); + string rabundFileName = getOutputFileName("rabund", variables); + if (countfile != "") { variables["[tag2]"] = "unique_list"; } + string listFileName = getOutputFileName("list", variables); + + if (countfile == "") { + m->openOutputFile(sabundFileName, outSabund); + m->openOutputFile(rabundFileName, outRabund); + outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName); + outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName); + + } + m->openOutputFile(listFileName, outList); + outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName); + + int count = 1; //start at leaves of tree and work towards root, processing the labels the user wants while((!done) && ((allLines == 1) || (labels.size() != 0))) { @@ -213,8 +257,8 @@ int PhylotypeCommand::execute(){ count++; if (m->control_pressed) { - outRabund.close(); outSabund.close(); outList.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + if (countfile == "") { outRabund.close(); outSabund.close(); } outList.close(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete tree; return 0; } @@ -226,6 +270,7 @@ int PhylotypeCommand::execute(){ ListVector list; list.setLabel(level); + //go through nodes and build listvector for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) { @@ -238,27 +283,35 @@ int PhylotypeCommand::execute(){ //make the names compatable with listvector string name = ""; for (int i = 0; i < names.size(); i++) { - if (namefile != "") { - map::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile - - if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile - else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1); } - - }else{ name += names[i] + ","; } + + if (names[i] != "unknown") { + if (namefile != "") { + map::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile + + if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile + else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + + }else{ name += names[i] + ","; } + } } + + if (m->control_pressed) { break; } + name = name.substr(0, name.length()-1); //rip off extra ',' - //add bin to list vector - list.push_back(name); + if (name != "") { list.push_back(name); } //caused by unknown } //print listvector - list.print(outList); - //print rabund - list.getRAbundVector().print(outRabund); - //print sabund - list.getSAbundVector().print(outSabund); - + if (!m->printedListHeaders) { list.printHeaders(outList); } + list.print(outList); + + if (countfile == "") { + //print rabund + list.getRAbundVector().print(outRabund); + //print sabund + list.getSAbundVector().print(outSabund); + } labels.erase(level); }else { @@ -279,13 +332,15 @@ int PhylotypeCommand::execute(){ } outList.close(); - outSabund.close(); - outRabund.close(); + if (countfile == "") { + outSabund.close(); + outRabund.close(); + } delete tree; if (m->control_pressed) { - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }