X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makebiomcommand.cpp;fp=makebiomcommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=acd0500963d096acfb5d1ea453cc9186feafe783;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp deleted file mode 100644 index acd0500..0000000 --- a/makebiomcommand.cpp +++ /dev/null @@ -1,643 +0,0 @@ -// -// makebiomcommand.cpp -// Mothur -// -// Created by Sarah Westcott on 4/16/12. -// Copyright (c) 2012 Schloss Lab. All rights reserved. -// - -#include "makebiomcommand.h" -#include "sharedrabundvector.h" -#include "inputdata.h" - -//taken from http://biom-format.org/documentation/biom_format.html -/* Minimal Sparse - { - "id":null, - "format": "Biological Observation Matrix 0.9.1", - "format_url": "http://biom-format.org", - "type": "OTU table", - "generated_by": "QIIME revision 1.4.0-dev", - "date": "2011-12-19T19:00:00", - "rows":[ - {"id":"GG_OTU_1", "metadata":null}, - {"id":"GG_OTU_2", "metadata":null}, - {"id":"GG_OTU_3", "metadata":null}, - {"id":"GG_OTU_4", "metadata":null}, - {"id":"GG_OTU_5", "metadata":null} - ], - "columns": [ - {"id":"Sample1", "metadata":null}, - {"id":"Sample2", "metadata":null}, - {"id":"Sample3", "metadata":null}, - {"id":"Sample4", "metadata":null}, - {"id":"Sample5", "metadata":null}, - {"id":"Sample6", "metadata":null} - ], - "matrix_type": "sparse", - "matrix_element_type": "int", - "shape": [5, 6], - "data":[[0,2,1], - [1,0,5], - [1,1,1], - [1,3,2], - [1,4,3], - [1,5,1], - [2,2,1], - [2,3,4], - [2,4,2], - [3,0,2], - [3,1,1], - [3,2,1], - [3,5,1], - [4,1,1], - [4,2,1] - ] - } - */ -/* Minimal dense - { - "id":null, - "format": "Biological Observation Matrix 0.9.1", - "format_url": "http://biom-format.org", - "type": "OTU table", - "generated_by": "QIIME revision 1.4.0-dev", - "date": "2011-12-19T19:00:00", - "rows":[ - {"id":"GG_OTU_1", "metadata":null}, - {"id":"GG_OTU_2", "metadata":null}, - {"id":"GG_OTU_3", "metadata":null}, - {"id":"GG_OTU_4", "metadata":null}, - {"id":"GG_OTU_5", "metadata":null} - ], - "columns": [ - {"id":"Sample1", "metadata":null}, - {"id":"Sample2", "metadata":null}, - {"id":"Sample3", "metadata":null}, - {"id":"Sample4", "metadata":null}, - {"id":"Sample5", "metadata":null}, - {"id":"Sample6", "metadata":null} - ], - "matrix_type": "dense", - "matrix_element_type": "int", - "shape": [5,6], - "data": [[0,0,1,0,0,0], - [5,1,0,2,3,1], - [0,0,1,4,2,0], - [2,1,1,0,0,1], - [0,1,1,0,0,0]] - } - */ -//********************************************************************************************************************** -vector MakeBiomCommand::setParameters(){ - try { - CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared); - CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcontaxonomy); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - 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 pmatrixtype("matrixtype", "Multiple", "sparse-dense", "sparse", "", "", "",false,false); parameters.push_back(pmatrixtype); - - vector myArray; - for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } - return myArray; - } - catch(exception& e) { - m->errorOut(e, "MakeBiomCommand", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string MakeBiomCommand::getHelpString(){ - try { - string helpString = ""; - helpString += "The make.biom command parameters are shared, contaxonomy, groups, matrixtype and label. shared is required, unless you have a valid current file.\n"; - helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n"; - helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n"; - helpString += "The matrixtype parameter allows you to select what type you would like to make. Choices are sparse and dense, default is sparse.\n"; - helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance. ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled.\n"; - helpString += "The make.biom command should be in the following format: make.biom(shared=yourShared, groups=yourGroups, label=yourLabels).\n"; - helpString += "Example make.biom(shared=abrecovery.an.shared, groups=A-B-C).\n"; - helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n"; - helpString += "The make.biom command outputs a .biom file.\n"; - helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; - return helpString; - } - catch(exception& e) { - m->errorOut(e, "MakeBiomCommand", "getHelpString"); - exit(1); - } -} -//********************************************************************************************************************** -MakeBiomCommand::MakeBiomCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["biom"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "MakeBiomCommand", "MakeBiomCommand"); - exit(1); - } -} -//********************************************************************************************************************** -MakeBiomCommand::MakeBiomCommand(string option) { - try { - abort = false; calledHelp = false; - allLines = 1; - - //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(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - map::iterator it; - - ValidParameters validParameter; - - //check to make sure all parameters are valid for command - for (it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - //initialize outputTypes - vector tempOutNames; - outputTypes["biom"] = 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 = ""; } - else { - string path; - it = parameters.find("shared"); - //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["shared"] = inputDir + it->second; } - } - - it = parameters.find("contaxonomy"); - //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["contaxonomy"] = inputDir + it->second; } - } - } - - //get shared file - sharedfile = validParameter.validFile(parameters, "shared", true); - if (sharedfile == "not open") { sharedfile = ""; abort = true; } - else if (sharedfile == "not found") { - //if there is a current shared file, use it - sharedfile = m->getSharedFile(); - if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } - else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } - }else { m->setSharedFile(sharedfile); } - - - //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 = m->hasPath(sharedfile); } - - contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true); - if (contaxonomyfile == "not found") { contaxonomyfile = ""; } - else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; } - - - //check for optional parameter and set defaults - // ...at some point should added some additional type checking... - label = validParameter.validFile(parameters, "label", false); - if (label == "not found") { label = ""; } - else { - if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } - else { allLines = 1; } - } - - groups = validParameter.validFile(parameters, "groups", false); - if (groups == "not found") { groups = ""; } - else { - m->splitAtDash(groups, Groups); - m->setGroups(Groups); - } - - if ((contaxonomyfile != "") && (labels.size() > 1)) { m->mothurOut("[ERROR]: the contaxonomy parameter cannot be used with multiple labels."); m->mothurOutEndLine(); abort = true; } - - format = validParameter.validFile(parameters, "matrixtype", false); if (format == "not found") { format = "sparse"; } - - if ((format != "sparse") && (format != "dense")) { - m->mothurOut(format + " is not a valid option for the matrixtype parameter. Options are sparse and dense."); m->mothurOutEndLine(); abort = true; - } - } - - } - catch(exception& e) { - m->errorOut(e, "MakeBiomCommand", "MakeBiomCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -int MakeBiomCommand::execute(){ - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - InputData input(sharedfile, "sharedfile"); - vector lookup = input.getSharedRAbundVectors(); - string lastLabel = lookup[0]->getLabel(); - - //if user did not specify a label, then use first one - if ((contaxonomyfile != "") && (labels.size() == 0)) { - allLines = 0; - labels.insert(lastLabel); - } - - //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. - set processedLabels; - set userLabels = labels; - - //as long as you are not at the end of the file or done wih the lines you want - while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } - - if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ - - m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - getBiom(lookup); - - processedLabels.insert(lookup[0]->getLabel()); - userLabels.erase(lookup[0]->getLabel()); - } - - if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - string saveLabel = lookup[0]->getLabel(); - - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } - lookup = input.getSharedRAbundVectors(lastLabel); - m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - - getBiom(lookup); - - processedLabels.insert(lookup[0]->getLabel()); - userLabels.erase(lookup[0]->getLabel()); - - //restore real lastlabel to save below - lookup[0]->setLabel(saveLabel); - } - - lastLabel = lookup[0]->getLabel(); - - //prevent memory leak and get next set - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } - lookup = input.getSharedRAbundVectors(); - } - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - //output error messages about any remaining user labels - set::iterator it; - bool needToRun = false; - for (it = userLabels.begin(); it != userLabels.end(); it++) { - m->mothurOut("Your file does not include the label " + *it); - if (processedLabels.count(lastLabel) != 1) { - m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); - needToRun = true; - }else { - m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); - } - } - - //run last label if you need to - if (needToRun == true) { - for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } - lookup = input.getSharedRAbundVectors(lastLabel); - - m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - getBiom(lookup); - - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } - } - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - //set sabund file as new current sabundfile - string current = ""; - itTypes = outputTypes.find("biom"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setBiomFile(current); } - } - - - 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) { - m->errorOut(e, "MakeBiomCommand", "execute"); - exit(1); - } -} -//********************************************************************************************************************** -int MakeBiomCommand::getBiom(vector& lookup){ - try { - - string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".biom"; - ofstream out; - m->openOutputFile(outputFileName, out); - outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName); - - string mothurString = "mothur" + toString(m->getVersion()); - time_t rawtime; - struct tm * timeinfo; - time ( &rawtime ); - timeinfo = localtime ( &rawtime ); - string dateString = asctime (timeinfo); - int pos = dateString.find('\n'); - if (pos != string::npos) { dateString = dateString.substr(0, pos);} - string spaces = " "; - - //standard - out << "{\n" + spaces + "\"id\":\"" + sharedfile + "-" + lookup[0]->getLabel() + "\",\n" + spaces + "\"format\": \"Biological Observation Matrix 0.9.1\",\n" + spaces + "\"format_url\": \"http://biom-format.org\",\n"; - out << spaces + "\"type\": \"OTU table\",\n" + spaces + "\"generated_by\": \"" << mothurString << "\",\n" + spaces + "\"date\": \"" << dateString << "\",\n"; - - vector metadata = getMetaData(lookup); - - if (m->control_pressed) { out.close(); return 0; } - - //get row info - /*"rows":[ - {"id":"GG_OTU_1", "metadata":null}, - {"id":"GG_OTU_2", "metadata":null}, - {"id":"GG_OTU_3", "metadata":null}, - {"id":"GG_OTU_4", "metadata":null}, - {"id":"GG_OTU_5", "metadata":null} - ],*/ - out << spaces + "\"rows\":[\n"; - string rowFront = spaces + spaces + "{\"id\":\""; - string rowBack = "\", \"metadata\":"; - for (int i = 0; i < m->currentBinLabels.size()-1; i++) { - if (m->control_pressed) { out.close(); return 0; } - out << rowFront << m->currentBinLabels[i] << rowBack << metadata[i] << "},\n"; - } - out << rowFront << m->currentBinLabels[(m->currentBinLabels.size()-1)] << rowBack << metadata[(m->currentBinLabels.size()-1)] << "}\n" + spaces + "],\n"; - - //get column info - /*"columns": [ - {"id":"Sample1", "metadata":null}, - {"id":"Sample2", "metadata":null}, - {"id":"Sample3", "metadata":null}, - {"id":"Sample4", "metadata":null}, - {"id":"Sample5", "metadata":null}, - {"id":"Sample6", "metadata":null} - ],*/ - - string colBack = "\", \"metadata\":null}"; - out << spaces + "\"columns\":[\n"; - for (int i = 0; i < lookup.size()-1; i++) { - if (m->control_pressed) { out.close(); return 0; } - out << rowFront << lookup[i]->getGroup() << colBack << ",\n"; - } - out << rowFront << lookup[(lookup.size()-1)]->getGroup() << colBack << "\n" + spaces + "],\n"; - - out << spaces + "\"matrix_type\": \"" << format << "\",\n" + spaces + "\"matrix_element_type\": \"int\",\n"; - out << spaces + "\"shape\": [" << m->currentBinLabels.size() << "," << lookup.size() << "],\n"; - out << spaces + "\"data\": ["; - - vector dataRows; - if (format == "sparse") { - /*"data":[[0,2,1], - [1,0,5], - [1,1,1], - [1,3,2], - [1,4,3], - [1,5,1], - [2,2,1], - [2,3,4], - [2,4,2], - [3,0,2], - [3,1,1], - [3,2,1], - [3,5,1], - [4,1,1], - [4,2,1] - ]*/ - string output = ""; - for (int i = 0; i < lookup[0]->getNumBins(); i++) { - - if (m->control_pressed) { out.close(); return 0; } - - for (int j = 0; j < lookup.size(); j++) { - string binInfo = "[" + toString(i) + "," + toString(j) + "," + toString(lookup[j]->getAbundance(i)) + "]"; - //only print non zero values - if (lookup[j]->getAbundance(i) != 0) { dataRows.push_back(binInfo); } - } - } - }else { - - /* "matrix_type": "dense", - "matrix_element_type": "int", - "shape": [5,6], - "data": [[0,0,1,0,0,0], - [5,1,0,2,3,1], - [0,0,1,4,2,0], - [2,1,1,0,0,1], - [0,1,1,0,0,0]]*/ - - for (int i = 0; i < lookup[0]->getNumBins(); i++) { - - if (m->control_pressed) { out.close(); return 0; } - - string binInfo = "["; - for (int j = 0; j < lookup.size()-1; j++) { - binInfo += toString(lookup[j]->getAbundance(i)) + ","; - } - binInfo += toString(lookup[lookup.size()-1]->getAbundance(i)) + "]"; - dataRows.push_back(binInfo); - } - } - - for (int i = 0; i < dataRows.size()-1; i++) { - out << dataRows[i] << ",\n" + spaces + spaces; - } - out << dataRows[dataRows.size()-1] << "]\n"; - - out << "}\n"; - out.close(); - - return 0; - } - catch(exception& e) { - m->errorOut(e, "MakeBiomCommand", "getBiom"); - exit(1); - } -} -//********************************************************************************************************************** -vector MakeBiomCommand::getMetaData(vector& lookup){ - try { - vector metadata; - - if (contaxonomyfile == "") { for (int i = 0; i < lookup[0]->getNumBins(); i++) { metadata.push_back("null"); } } - else { - - //read constaxonomy file storing in a map, otulabel -> taxonomy - //constaxonomy file will most likely contain more labels than the shared file, because sharedfile could have been subsampled. - ifstream in; - m->openInputFile(contaxonomyfile, in); - - //grab headers - m->getline(in); m->gobble(in); - - string otuLabel, tax; - int size; - vector otuLabels; - vector taxs; - while (!in.eof()) { - - if (m->control_pressed) { in.close(); return metadata; } - - in >> otuLabel >> size >> tax; m->gobble(in); - - otuLabels.push_back(otuLabel); - taxs.push_back(tax); - } - in.close(); - - //should the labels be Otu001 or PhyloType001 - string firstBin = m->currentBinLabels[0]; - string binTag = "Otu"; - if ((firstBin.find("Otu")) == string::npos) { binTag = "PhyloType"; } - - //convert list file bin labels to shared file bin labels - //parse tax strings - //save in map - map labelTaxMap; - string snumBins = toString(otuLabels.size()); - for (int i = 0; i < otuLabels.size(); i++) { - - if (m->control_pressed) { return metadata; } - - //if there is a bin label use it otherwise make one - string binLabel = binTag; - string sbinNumber = otuLabels[i]; - if (sbinNumber.length() < snumBins.length()) { - int diff = snumBins.length() - sbinNumber.length(); - for (int h = 0; h < diff; h++) { binLabel += "0"; } - } - binLabel += sbinNumber; - - labelTaxMap[binLabel] = taxs[i]; - } - - - //{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]} - - //traverse the binLabels forming the metadata strings and saving them - //make sure to sanity check - map::iterator it; - for (int i = 0; i < m->currentBinLabels.size(); i++) { - - if (m->control_pressed) { return metadata; } - - it = labelTaxMap.find(m->currentBinLabels[i]); - - if (it == labelTaxMap.end()) { m->mothurOut("[ERROR]: can't find taxonomy information for " + m->currentBinLabels[i] + ".\n"); m->control_pressed = true; } - else { - vector bootstrapValues; - string data = "{\"taxonomy\":["; - - vector scores; - vector taxonomies = parseTax(it->second, scores); - - for (int j = 0; j < taxonomies.size()-1; j ++) { data += "\"" + taxonomies[j] + "\", "; } - data += "\"" + taxonomies[taxonomies.size()-1] + "\"]"; - - //add bootstrap values if available - if (scores[0] != "null") { - data += ", \"bootstrap\":["; - - for (int j = 0; j < scores.size()-1; j ++) { data += scores[j] + ", "; } - data += scores[scores.size()-1] + "]"; - - } - data += "}"; - - metadata.push_back(data); - } - } - } - - return metadata; - - } - catch(exception& e) { - m->errorOut(e, "MakeBiomCommand", "getMetadata"); - exit(1); - } - -} -/**************************************************************************************************/ -//returns {Bacteria, Bacteroidetes, ..} and scores is filled with {100, 98, ...} or {null, null, null} -vector MakeBiomCommand::parseTax(string tax, vector& scores) { - try { - - string taxon; - vector taxs; - - while (tax.find_first_of(';') != -1) { - - if (m->control_pressed) { return taxs; } - - //get taxon - taxon = tax.substr(0,tax.find_first_of(';')); - - int pos = taxon.find_last_of('('); - if (pos != -1) { - //is it a number? - int pos2 = taxon.find_last_of(')'); - if (pos2 != -1) { - string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1))); - if (m->isNumeric1(confidenceScore)) { - taxon = taxon.substr(0, pos); //rip off confidence - scores.push_back(confidenceScore); - }else{ scores.push_back("null"); } - } - } - - //strip "" if they are there - pos = taxon.find("\""); - if (pos != string::npos) { - string newTax = ""; - for (int k = 0; k < taxon.length(); k++) { - if (taxon[k] != '\"') { newTax += taxon[k]; } - } - taxon = newTax; - } - - //look for bootstrap value - taxs.push_back(taxon); - tax = tax.substr(tax.find_first_of(';')+1, tax.length()); - } - - return taxs; - } - catch(exception& e) { - m->errorOut(e, "MakeBiomCommand", "parseTax"); - exit(1); - } -} - -//********************************************************************************************************************** - - -