X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=otuassociationcommand.cpp;h=23cac294cad4f1b25caa0e4f4d55de40f1fb2876;hp=93f46ba1e716f80e321245832eb11eabb2bda733;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hpb=05c52893c6c2467381fe7e7b769d86b6209af2e1 diff --git a/otuassociationcommand.cpp b/otuassociationcommand.cpp index 93f46ba..23cac29 100644 --- a/otuassociationcommand.cpp +++ b/otuassociationcommand.cpp @@ -13,14 +13,15 @@ //********************************************************************************************************************** vector OTUAssociationCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared); - CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund); - CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false,true); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false); parameters.push_back(prelabund); + CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata); + CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false,true); parameters.push_back(pmethod); + 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); } @@ -37,9 +38,10 @@ string OTUAssociationCommand::getHelpString(){ string helpString = ""; helpString += "The otu.association command reads a shared or relabund file and calculates the correlation coefficients between otus.\n"; helpString += "If you provide a metadata file, mothur will calculate te correlation bewteen the metadata and the otus.\n"; - helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method and label. The shared or relabund parameter is required.\n"; + helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method, cutoff and label. The shared or relabund parameter is required.\n"; helpString += "The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n"; helpString += "The label parameter allows you to select what distances level you would like used, and are also separated by dashes.\n"; + helpString += "The cutoff parameter allows you to set a pvalue at which the otu will be reported.\n"; helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n"; helpString += "The otu.association command should be in the following format: otu.association(shared=yourSharedFile, method=yourMethod).\n"; helpString += "Example otu.association(shared=genus.pool.shared, method=kendall).\n"; @@ -53,12 +55,27 @@ string OTUAssociationCommand::getHelpString(){ } } //********************************************************************************************************************** +string OTUAssociationCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "otucorr") { pattern = "[filename],[distance],[tag],otu.corr"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "OTUAssociationCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** OTUAssociationCommand::OTUAssociationCommand(){ try { abort = true; calledHelp = true; setParameters(); vector tempOutNames; - outputTypes["otu.corr"] = tempOutNames; + outputTypes["otucorr"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand"); @@ -90,7 +107,7 @@ OTUAssociationCommand::OTUAssociationCommand(string option) { } vector tempOutNames; - outputTypes["otu.corr"] = tempOutNames; + outputTypes["otucorr"] = 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); @@ -175,6 +192,10 @@ OTUAssociationCommand::OTUAssociationCommand(string option) { method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; } + string temp = validParameter.validFile(parameters, "cutoff", false); + if (temp == "not found") { temp = "10"; } + m->mothurConvert(temp, cutoff); + if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; } } @@ -305,9 +326,12 @@ int OTUAssociationCommand::processShared(){ //********************************************************************************************************************** int OTUAssociationCommand::process(vector& lookup){ try { - - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr"; - outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName)); + variables["[distance]"] = lookup[0]->getLabel(); + variables["[tag]"] = method; + string outputFileName = getOutputFileName("otucorr",variables); + outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName); ofstream out; m->openOutputFile(outputFileName, out); @@ -336,7 +360,7 @@ int OTUAssociationCommand::process(vector& lookup){ else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); } else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; } - out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; + if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; } } } }else { //compare otus to metadata @@ -353,7 +377,7 @@ int OTUAssociationCommand::process(vector& lookup){ else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); } else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; } - out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; + if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; } } } @@ -466,8 +490,12 @@ int OTUAssociationCommand::processRelabund(){ int OTUAssociationCommand::process(vector& lookup){ try { - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr"; - outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName)); + variables["[distance]"] = lookup[0]->getLabel(); + variables["[tag]"] = method; + string outputFileName = getOutputFileName("otucorr",variables); + outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName); ofstream out; m->openOutputFile(outputFileName, out); @@ -495,7 +523,7 @@ int OTUAssociationCommand::process(vector& lookup){ else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); } else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; } - out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; + if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; } } } }else { //compare otus to metadata @@ -512,7 +540,7 @@ int OTUAssociationCommand::process(vector& lookup){ else if (method == "kendall") { coef = linear.calcKendall(xy[i], metadata[k], sig); } else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; } - out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; + if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; } } }