+++ /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, 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<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["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<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; }
-
- //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<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, 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;
-
- 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<string, 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 {
- vector<string> bootstrapValues;
- string data = "{\"taxonomy\":[";
-
- vector<string> scores;
- vector<string> 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<string> MakeBiomCommand::parseTax(string tax, vector<string>& scores) {
- try {
-
- string taxon;
- vector<string> 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);
- }
-}
-
-//**********************************************************************************************************************
-
-
-
projects / mothur.git / blobdiff