X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=2018170648761a91b5b9026fada7079b0b4e73e1;hb=3e2465c16d187247ce3befd29811c2d5dfc15ee8;hp=2dbd53a5dad36477279961d76d547fff3d8e83d3;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp index 2dbd53a..2018170 100644 --- a/phylotypecommand.cpp +++ b/phylotypecommand.cpp @@ -13,8 +13,58 @@ #include "rabundvector.hpp" #include "sabundvector.hpp" +//********************************************************************************************************************** +vector PhylotypeCommand::getValidParameters(){ + try { + string Array[] = {"taxonomy","cutoff","label","name","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PhylotypeCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +PhylotypeCommand::PhylotypeCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; + outputTypes["rabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector PhylotypeCommand::getRequiredParameters(){ + try { + string Array[] = {"taxonomy"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PhylotypeCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector PhylotypeCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PhylotypeCommand", "getRequiredFiles"); + exit(1); + } +} /**********************************************************************************************************************/ -PhylotypeCommand::PhylotypeCommand(string option){ +PhylotypeCommand::PhylotypeCommand(string option) { try { abort = false; @@ -24,7 +74,7 @@ PhylotypeCommand::PhylotypeCommand(string option){ else { //valid paramters for this command - string AlignArray[] = {"taxonomy","cutoff","label","outputdir","inputdir"}; + string AlignArray[] = {"taxonomy","cutoff","label","name","outputdir","inputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); OptionParser parser(option); @@ -38,6 +88,12 @@ PhylotypeCommand::PhylotypeCommand(string option){ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; + outputTypes["rabund"] = tempOutNames; + //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 = ""; } @@ -46,23 +102,36 @@ PhylotypeCommand::PhylotypeCommand(string option){ it = parameters.find("taxonomy"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } + + 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; } + } } taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true); if (taxonomyFileName == "not found") { - mothurOut("taxonomy is a required parameter for the phylotype command."); - mothurOutEndLine(); + m->mothurOut("taxonomy is a required parameter for the phylotype command."); + m->mothurOutEndLine(); abort = true; }else if (taxonomyFileName == "not open") { abort = true; } + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { readNamesFile(); } + //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 = ""; - outputDir += hasPath(taxonomyFileName); //if user entered a file with a path then preserve it + outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it } string temp = validParameter.validFile(parameters, "cutoff", false); @@ -72,14 +141,14 @@ PhylotypeCommand::PhylotypeCommand(string option){ label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; allLines = 1; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } } } catch(exception& e) { - errorOut(e, "PhylotypeCommand", "PhylotypeCommand"); + m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand"); exit(1); } } @@ -87,19 +156,19 @@ PhylotypeCommand::PhylotypeCommand(string option){ void PhylotypeCommand::help(){ try { - mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n"); - mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n"); - mothurOut("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"); - mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n"); - mothurOut("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"); - mothurOut("The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n"); - mothurOut("For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n"); - mothurOut("The phylotype command should be in the following format: \n"); - mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n"); - mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n"); + m->mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n"); + m->mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n"); + m->mothurOut("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"); + m->mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n"); + m->mothurOut("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"); + m->mothurOut("The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n"); + m->mothurOut("For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n"); + m->mothurOut("The phylotype command should be in the following format: \n"); + m->mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n"); + m->mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n"); } catch(exception& e) { - errorOut(e, "PhylotypeCommand", "help"); + m->errorOut(e, "PhylotypeCommand", "help"); exit(1); } } @@ -117,7 +186,9 @@ int PhylotypeCommand::execute(){ //reads in taxonomy file and makes all the taxonomies the same length //by appending the last taxon to a given taxonomy as many times as needed to //make it as long as the longest taxonomy in the file - TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff); + TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir); + + if (m->control_pressed) { delete taxEqual; return 0; } string equalizedTaxFile = taxEqual->getEqualizedTaxFile(); @@ -131,19 +202,25 @@ int PhylotypeCommand::execute(){ for (int i = 0; i < leaves.size(); i++) { currentNodes[leaves[i]] = leaves[i]; } bool done = false; - if (tree->get(leaves[0]).parent == -1) { mothurOut("Empty Tree"); mothurOutEndLine(); done = true; } + if (tree->get(leaves[0]).parent == -1) { m->mothurOut("Empty Tree"); m->mothurOutEndLine(); done = true; } + + if (m->control_pressed) { delete tree; return 0; } - string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName)); + string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName)); ofstream outList; string outputListFile = fileroot + "tx.list"; - openOutputFile(outputListFile, outList); + m->openOutputFile(outputListFile, outList); ofstream outSabund; string outputSabundFile = fileroot + "tx.sabund"; - openOutputFile(outputSabundFile, outSabund); + m->openOutputFile(outputSabundFile, outSabund); ofstream outRabund; string outputRabundFile = fileroot + "tx.rabund"; - openOutputFile(outputRabundFile, outRabund); + 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); int count = 1; //start at leaves of tree and work towards root, processing the labels the user wants @@ -152,11 +229,17 @@ int PhylotypeCommand::execute(){ string level = toString(count); count++; + if (m->control_pressed) { + outRabund.close(); outSabund.close(); outList.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + delete tree; return 0; + } + //is this a level the user want output for if(allLines == 1 || labels.count(level) == 1){ //output level - mothurOut(level); mothurOutEndLine(); + m->mothurOut(level); m->mothurOutEndLine(); ListVector list; list.setLabel(level); @@ -171,7 +254,15 @@ int PhylotypeCommand::execute(){ //make the names compatable with listvector string name = ""; - for (int i = 0; i < names.size(); i++) { name += names[i] + ","; } + 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] + ","; } + } name = name.substr(0, name.length()-1); //rip off extra ',' //add bin to list vector @@ -210,12 +301,50 @@ int PhylotypeCommand::execute(){ delete tree; + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 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(); + return 0; } catch(exception& e) { - errorOut(e, "PhylotypeCommand", "execute"); + m->errorOut(e, "PhylotypeCommand", "execute"); exit(1); } } +/*****************************************************************/ +int PhylotypeCommand::readNamesFile() { + try { + + ifstream in; + m->openInputFile(namefile, in); + + string first, second; + map::iterator itNames; + + while(!in.eof()) { + in >> first >> second; m->gobble(in); + + itNames = namemap.find(first); + if (itNames == namemap.end()) { + namemap[first] = second; + }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; } + } + in.close(); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "PhylotypeCommand", "readNamesFile"); + exit(1); + } +} + /**********************************************************************************************************************/