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app.js
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// This is an example of an angular application, using angularjs-genoverse
(function() {
angular.module("Example", ["Genoverse"]);
/**
* Turn on html5mode only in modern browsers because
* in the older ones html5mode rewrites urls with Hangbangs
* which break normal Django pages.
* With html5mode off IE lt 10 will be able to navigate the site
* but won't be able to open deep links to Angular pages
* (for example, a link to a search result won't load in IE 9).
*/
angular.module('Example').config(['$locationProvider', function($locationProvider) {
if (window.history && window.history.pushState) {
$locationProvider.html5Mode(true);
}
}]);
angular.module('Example').controller('GenoverseGenomeBrowser', ['$scope', '$location', '$filter', function ($scope, $location, $filter) {
// Constructor
// -----------
$scope.genomes = [
// Ensembl
{
'ensemblSpecies': 'homo_sapiens',
'species': 'Homo sapiens',
'synonyms': ['human'],
'assembly': 'GRCh38',
'assembly_ucsc': 'hg38',
'taxid': 9606,
'division': 'Ensembl',
'example_location': {
'chromosome': 'X',
'start': 73819307,
'end': 73856333
}
},
{
'ensemblSpecies': 'mus_musculus',
'species': 'Mus musculus',
'synonyms': ['mouse'],
'assembly': 'GRCm38',
'assembly_ucsc': 'mm10',
'taxid': 10090,
'division': 'Ensembl',
'example_location': {
'chromosome': 1,
'start': 86351908,
'end': 86352200
}
},
{
'ensemblSpecies': 'danio_rerio',
'species': 'Danio rerio',
'synonyms': ['zebrafish'],
'assembly': 'GRCz10',
'assembly_ucsc': 'danRer10',
'taxid': 7955,
'division': 'Ensembl',
'example_location': {
'chromosome': 9,
'start': 7633910,
'end': 7634210
}
},
{
'ensemblSpecies': 'bos_taurus',
'species': 'Bos taurus',
'synonyms': ['cow'],
'assembly': 'UMD3.1',
'assembly_ucsc': 'bosTau6',
'taxid': 9913,
'division': 'Ensembl',
'example_location': {
'chromosome': 15,
'start': 82197673,
'end': 82197837
}
},
{
'ensemblSpecies': 'rattus_norvegicus',
'species': 'Rattus norvegicus',
'synonyms': ['rat'],
'assembly': 'Rnor_6.0',
'assembly_ucsc': 'rn6',
'taxid': 10116,
'division': 'Ensembl',
'example_location': {
'chromosome': 'X',
'start': 118277628,
'end': 118277850
}
},
// {
// 'ensemblSpecies': 'felis_catus',
// 'species': 'Felis catus',
// 'synonyms': ['cat'],
// 'assembly': 'Felis_catus_6.2',
// 'assembly_ucsc': 'felCat5',
// 'taxid': 9685,
// 'division': 'Ensembl',
// 'example_location': {
// 'chromosome': 'X',
// 'start': 18058223,
// 'end': 18058546
// }
// },
// {
// 'ensemblSpecies': 'macaca_mulatta',
// 'species': 'Macaca mulatta',
// 'synonyms': ['macaque'],
// 'assembly': 'MMUL_1',
// 'assembly_ucsc': '', # no matching assembly
// 'taxid': 9544,
// 'division': 'Ensembl',
// 'example_location': {
// 'chromosome': 1,
// 'start': 146238837,
// 'end': 146238946
// }
// },
{
'ensemblSpecies': 'pan_troglodytes',
'species': 'Pan troglodytes',
'synonyms': ['chimp'],
'assembly': 'CHIMP2.1.4',
'assembly_ucsc': 'panTro4',
'taxid': 9598,
'division': 'Ensembl',
'example_location': {
'chromosome': 11,
'start': 78369004,
'end': 78369219
}
},
{
'ensemblSpecies': 'canis_lupus_familiaris',
'species': 'Canis familiaris',
'synonyms': ['dog', 'Canis lupus familiaris'],
'assembly': 'CanFam3.1',
'assembly_ucsc': 'canFam3',
'taxid': 9615,
'division': 'Ensembl',
'example_location': {
'chromosome': 19,
'start': 22006909,
'end': 22007119
}
},
// {
// 'ensemblSpecies': 'gallus_gallus',
// 'species': 'Gallus gallus',
// 'synonyms': ['chicken'],
// 'assembly': 'Galgal4',
// 'assembly_ucsc': 'galGal4',
// 'taxid': 9031,
// 'division': 'Ensembl',
// 'example_location': {
// 'chromosome': 9,
// 'start': 15676031,
// 'end': 15676160
// }
// },
// {
// 'ensemblSpecies': 'xenopus_tropicalis',
// 'species': 'Xenopus tropicalis',
// 'synonyms': ['frog'],
// 'assembly': 'JGI_4.2',
// 'assembly_ucsc': 'xenTro3',
// 'taxid': 8364,
// 'division': 'Ensembl',
// 'example_location': {
// 'chromosome': 'NC_006839',
// 'start': 11649,
// 'end': 11717
// }
// },
// Ensembl Fungi
// {
// 'ensemblSpecies': 'saccharomyces_cerevisiae',
// 'species': 'Saccharomyces cerevisiae',
// 'synonyms': ['budding yeast', 'Saccharomyces cerevisiae S288c'],
// 'assembly': 'R64-1-1',
// 'assembly_ucsc': '',
// 'taxid': 559292,
// 'division': 'Ensembl Fungi',
// 'example_location': {
// 'chromosome': 'XII',
// 'start': 856709,
// 'end': 856919
// }
// },
{
'ensemblSpecies': 'schizosaccharomyces_pombe',
'species': 'Schizosaccharomyces pombe',
'synonyms': ['fission yeast'],
'assembly': 'ASM294v2',
'assembly_ucsc': '',
'taxid': 4896,
'division': 'Ensembl Fungi',
'example_location': {
'chromosome': 'I',
'start': 540951,
'end': 544327
}
},
// Ensembl Metazoa
{
'ensemblSpecies': 'caenorhabditis_elegans',
'species': 'Caenorhabditis elegans',
'synonyms': ['worm'],
'assembly': 'WBcel235',
'assembly_ucsc': 'ce11',
'taxid': 6239,
'division': 'Ensembl Metazoa',
'example_location': {
'chromosome': 'III',
'start': 11467363,
'end': 11467705
}
},
{
'ensemblSpecies': 'drosophila_melanogaster',
'species': 'Drosophila melanogaster',
'synonyms': ['fly'],
'assembly': 'BDGP6',
'assembly_ucsc': 'dm6',
'taxid': 7227,
'division': 'Ensembl Metazoa',
'example_location': {
'chromosome': '3R',
'start': 7474331,
'end': 7475217
}
},
{
'ensemblSpecies': 'bombyx_mori',
'species': 'Bombyx mori',
'synonyms': ['silkworm'],
'assembly': 'GCA_000151625.1',
'assembly_ucsc': '',
'taxid': 7091,
'division': 'Ensembl Metazoa',
'example_location': {
'chromosome': 'scaf16',
'start': 6180018,
'end': 6180422
}
},
// {
// 'ensemblSpecies': 'anopheles_gambiae',
// 'species': 'Anopheles gambiae',
// 'synonyms': [],
// 'assembly': 'AgamP4',
// 'assembly_ucsc': '',
// 'taxid': 7165,
// 'division': 'Ensembl Metazoa',
// 'example_location': {
// 'chromosome': '2R',
// 'start': 34644956,
// 'end': 34645131
// }
// },
// Ensembl Protists
{
'ensemblSpecies': 'dictyostelium_discoideum',
'species': 'Dictyostelium discoideum',
'synonyms': [],
'assembly': 'dictybase.01',
'assembly_ucsc': '',
'taxid': 44689,
'division': 'Ensembl Protists',
'example_location': {
'chromosome': 2,
'start': 7874546,
'end': 7876498
}
},
// {
// 'ensemblSpecies': 'plasmodium_falciparum',
// 'species': 'Plasmodium falciparum',
// 'synonyms': [],
// 'assembly': 'ASM276v1',
// 'assembly_ucsc': '',
// 'taxid': 5833,
// 'division': 'Ensembl Protists',
// 'example_location': {
// 'chromosome': 13,
// 'start': 2796339,
// 'end': 2798488
// }
// },
// Ensembl Plants
{
'ensemblSpecies': 'arabidopsis_thaliana',
'species': 'Arabidopsis thaliana',
'synonyms': [],
'assembly': 'TAIR10',
'assembly_ucsc': '',
'taxid': 3702,
'division': 'Ensembl Plants',
'example_location': {
'chromosome': 2,
'start': 18819643,
'end': 18822629
}
}
];
$scope.genomeNames = [];
for (var i = 0; i < $scope.genomes.length; i++) {
$scope.genomeNames.push($scope.genomes[i].ensemblSpecies);
}
$scope.exampleLocations = {};
for (var i = 0; i < $scope.genomes.length; i++) {
$scope.exampleLocations[$scope.genomes[i].ensemblSpecies] = {
'chr': $scope.genomes[i].example_location.chromosome,
'start': $scope.genomes[i].example_location.start,
'end': $scope.genomes[i].example_location.end
}
}
$scope.genome = $scope.genomes[0].ensemblSpecies;
// get domain for Ensembl links
$scope.domain = getEnsemblSubdomainByDivision($scope.genome, $scope.genomes);
$scope.chromosome = "X";
$scope.start = 73819307;
$scope.end = 73856333;
$scope.Genoverse = Genoverse;
$scope.urls = {
sequence: function () { // Sequence track configuration
var species = $filter('urlencodeSpecies')($scope.genome);
var endpoint = getEndpoint(species);
return '__ENDPOINT__/sequence/region/__SPECIES__/__CHR__:__START__-__END__?content-type=text/plain'
.replace('__ENDPOINT__', endpoint)
.replace('__SPECIES__', species);
},
genes: function() { // Genes track configuration
var species = $filter('urlencodeSpecies')($scope.genome);
var endpoint = getEndpoint(species);
return '__ENDPOINT__/overlap/region/__SPECIES__/__CHR__:__START__-__END__?feature=gene;content-type=application/json'
.replace('__ENDPOINT__', endpoint)
.replace('__SPECIES__', species);
},
transcripts: function() { // Transcripts track configuration
var species = $filter('urlencodeSpecies')($scope.genome);
var endpoint = getEndpoint(species);
return '__ENDPOINT__/overlap/region/__SPECIES__/__CHR__:__START__-__END__?feature=transcript;feature=exon;feature=cds;content-type=application/json'
.replace('__ENDPOINT__', endpoint)
.replace('__SPECIES__', species);
}
};
// reflect any changes in genome in address bar
$scope.$watch('genome', setUrl);
$scope.$watch('chromosome', setUrl);
$scope.$watch('start', setUrl);
$scope.$watch('stop', setUrl);
$scope.$watch('genome', setDomain);
$scope.getGenomeObject = getGenomeObject;
// Method definitions
// ------------------
/**
* Sets the url in address bar to reflect the changes in browser location
*/
function setUrl(newValue, oldValue) {
// set the full url
$location.search({
species: $scope.genome,
chromosome: $scope.chromosome,
start: $scope.start,
end: $scope.end
});
$location.replace();
}
function setDomain(newValue, oldValue) {
$scope.domain = getEnsemblSubdomainByDivision(newValue, $scope.genomes);
}
/**
* Dynamically determine whether to use E! or EG REST API based on species.
* If species not in E!, use EG.
* Ensembl species list: http://www.ensembl.org/info/about/species.html
*/
function getEndpoint(species) {
var ensemblSpecies = [
"ailuropoda_melanoleuca",
"anas_platyrhynchos",
"anolis_carolinensis",
"astyanax_mexicanus",
"bos_taurus",
"callithrix_jacchus",
"canis_lupus_familiaris",
"cavia_porcellus",
"ceratotherium_simum_simum",
"chlorocebus_sabaeus",
"choloepus_hoffmanni",
"chrysemys_picta_bellii",
"ciona_intestinalis",
"ciona_savignyi",
"cricetulus_griseus",
"danio_rerio",
"dasypus_novemcinctus",
"dipodomys_ordii",
"drosophila_melanogaster",
"echinops_telfairi",
"equus_caballus",
"erinaceus_europaeus",
"felis_catus",
"ficedula_albicollis",
"gadus_morhua",
"gallus_gallus",
"gasterosteus_aculeatus",
"gorilla_gorilla_gorilla",
"heterocephalus_glaber",
"homo_sapiens",
"ictidomys_tridecemlineatus",
"latimeria_chalumnae",
"lepisosteus_oculatus",
"loxodonta_africana",
"macaca_fascicularis",
"macaca_mulatta",
"macropus_eugenii",
"meleagris_gallopavo",
"melopsittacus_undulatus",
"microcebus_murinus",
"microtus_ochrogaster",
"monodelphis_domestica",
"mus_musculus",
"mustela_putorius_furo",
"myotis_lucifugus",
"nomascus_leucogenys",
"ochotona_princeps",
"oreochromis_niloticus",
"ornithorhynchus_anatinus",
"orycteropus_afer_afer",
"oryctolagus_cuniculus",
"oryzias_latipes",
"otolemur_garnettii",
"ovis_aries",
"pan_troglodytes",
"papio_anubis",
"papio_hamadryas",
"pelodiscus_sinensis",
"petromyzon_marinus",
"poecilia_formosa",
"pongo_abelii",
"procavia_capensis",
"pteropus_vampyrus",
"rattus_norvegicus",
"saimiri_boliviensis",
"sarcophilus_harrisii",
"sorex_araneus",
"sus_scrofa",
"sus_scrofa_map",
"taeniopygia_guttata",
"takifugu_rubripes",
"tarsius_syrichta",
"tetraodon_nigroviridis",
"tupaia_belangeri",
"tursiops_truncatus",
"vicugna_pacos",
"xenopus_tropicalis",
"xiphophorus_maculatus"
];
// "saccharomyces_cerevisiae", "caenorhabditis_elegans"];
// "saccharomyces_cerevisiae", "caenorhabditis_elegans" could use either E! or EG
var encoded = $filter('urlencodeSpecies')(species); // urlencoded species name
return ensemblSpecies.indexOf(encoded) > -1 ? 'https://rest.ensembl.org' : 'https://rest.ensemblgenomes.org';
}
/**
* @param genome {String} - e.g. 'homo_sapient'
* @param genomes {Array} - contents of $scope.genome
* @returns {String} element of genomes array
*/
function getGenomeObject(genome, genomes) {
// get genome object from Genomes
var genomeObject;
for (var i = 0; i < $scope.genomes.length; i++) {
if (genome === $scope.genomes[i].ensemblSpecies) {
genomeObject = $scope.genomes[i];
return genomeObject;
}
}
// if we're here, this is a failure
console.log("Can't get genomeObject for genome: " + genome);
return null;
}
/**
* Takes a genome on input, looks into its division attribute and returns the corresponding Ensembl
* subdomain
*
* @param genome {String}
* @param genomes {Array} e.g.
* [{
* 'ensemblSpecies': 'mus_musculus', 'species': 'Mus musculus', 'synonyms': ['mouse'],
* 'assembly': 'GRCm38', 'assembly_ucsc': 'mm10',
* 'taxid': 10090, 'division': 'Ensembl',
* 'example_location': {'chromosome': 1, 'start': 86351981, 'end': 86352127,}
* }, ...]
* @returns {String} domain name without protocol or slashes or trailing dots
*/
function getEnsemblSubdomainByDivision(genome, genomes) {
var subdomain;
// get genome object from Genomes
var genomeObject = getGenomeObject(genome, genomes);
if (genomeObject.division == 'Ensembl') {
subdomain = 'ensembl.org';
} else if (genomeObject.division == 'Ensembl Plants') {
subdomain = 'plants.ensembl.org';
} else if (genomeObject.division == 'Ensembl Metazoa') {
subdomain = 'metazoa.ensembl.org';
} else if (genomeObject.division == 'Ensembl Bacteria') {
subdomain = 'bacteria.ensembl.org';
} else if (genomeObject.division == 'Ensembl Fungi') {
subdomain = 'fungi.ensembl.org';
} else if (genomeObject.division == 'Ensembl Protists') {
subdomain = 'protists.ensembl.org';
}
return subdomain;
}
}]);
})();