--- /dev/null
+//
+// 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<string> 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<string> 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, 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 make.biom command should be in the following format: make.biom(shared=yourShared, groups=yourGroups, label=yourLabels).\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 after the classify.otu command was run on the list and taxonomy file.\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<string> 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<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::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<string> tempOutNames;
+ outputTypes["relabund"] = 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<SharedRAbundVector*> 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<string> processedLabels;
+ set<string> 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<string>::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; }
+
+ 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<SharedRAbundVector*>& 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<string> 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<string> 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<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup){
+ try {
+ vector<string> 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<string> otuLabels;
+ vector<string> 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<string, vector<string> > 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;
+
+ vector<string> taxString;
+ m->splitAtChar(taxs[i], taxString, ';');
+ taxString.pop_back(); //adds blank string because taxonomies end in ;
+
+ labelTaxMap[binLabel] = taxString;
+ }
+
+
+ //{"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<string, vector<string> >::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 {
+ string data = "{\"taxonomy\":[";
+ for (int j = 0; j < (it->second).size()-1; j ++) {
+
+ string taxon = (it->second)[j];
+
+ //strip "" if they are there
+ int 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;
+ }
+
+ data += "\"" + taxon + "\", ";
+ }
+
+ string taxon = (it->second)[(it->second).size()-1];
+
+ //strip "" if they are there
+ int 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;
+ }
+
+ data += "\"" + taxon + "\"]} ";
+
+ metadata.push_back(data);
+ }
+ }
+ }
+
+ return metadata;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeBiomCommand", "getMetadata");
+ exit(1);
+ }
+
+}
+//**********************************************************************************************************************
+
+
+
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