@gmod/jbrowse
Version:
JBrowse - client-side genome browser
86 lines (76 loc) • 2.42 kB
JavaScript
require([
'dojo/_base/array',
'JBrowse/Browser'
], function( array, Browser ) {
describe( 'centralized ref seq name regularization', function() {
var b = new Browser({ unitTestMode: true });
var testCases = [
[ 'ctgA', 'ctga' ],
[ 'MT', 'chrm' ],
[ 'Pt', 'pt' ],
[ 'C9', 'c9' ],
[ 'chrM', 'chrm' ],
[ 'chrMT', 'chrm' ],
[ 'ChrC', 'chrc' ],
[ 'chrom01', 'chr1' ],
[ 'Bvchr1_un.sca002', 'bvchr1_un.sca002' ],
[ 'chr01', 'chr1' ],
[ 'CHROMOSOME11', 'chr11' ],
[ 'SCAFFOLD0231', 'scaffold231' ],
[ 'contig47', 'ctg47' ],
[ 'ctg47', 'ctg47' ],
[ 'Oryza_sativa_1234.01', 'oryza_sativa_1234.01' ],
[ '01', 'chr1' ],
[ '1', 'chr1' ],
[ 'chrI', 'chri' ] ,
[ 'chrII', 'chrii' ] ,
[ 'chrIII', 'chriii' ] ,
[ 'chrIV', 'chriv' ] ,
[ 'chrIX', 'chrix' ] ,
[ 'chrV', 'chrv' ] ,
[ 'chrVI', 'chrvi' ] ,
[ 'chrVII', 'chrvii' ] ,
[ 'chrVIII', 'chrviii' ] ,
[ 'chrX', 'chrx' ] ,
[ 'chrXI', 'chrxi' ] ,
[ 'chrXII', 'chrxii' ] ,
[ 'chrXIII', 'chrxiii' ] ,
[ 'chrXIV', 'chrxiv' ] ,
[ 'chrXV', 'chrxv' ] ,
[ 'chrXVI', 'chrxvi' ] ,
[ 'chrmt', 'chrm' ] ,
[ 'I', 'chri' ] ,
[ 'II', 'chrii' ] ,
[ 'III', 'chriii' ] ,
[ 'IV', 'chriv' ] ,
[ 'IX', 'chrix' ] ,
[ 'V', 'chrv' ] ,
[ 'VI', 'chrvi' ] ,
[ 'VII', 'chrvii' ] ,
[ 'VIII', 'chrviii' ] ,
[ 'X', 'chrx' ] ,
[ 'XI', 'chrxi' ] ,
[ 'XII', 'chrxii' ] ,
[ 'XIII', 'chrxiii' ] ,
[ 'XIV', 'chrxiv' ] ,
[ 'XV', 'chrxv' ] ,
[ 'XVI', 'chrxvi' ] ,
[ 'mt', 'chrm' ],
[ 'M', 'chrm' ],
[ 'chr2L', 'chr2l' ],
[ '2L', 'chr2l' ],
[ '2R', 'chr2r' ],
[ '2K', '2k' ]
];
array.forEach( testCases, function( testCase ) {
it( 'works for '+testCase[0], function() {
expect( b.regularizeReferenceName( testCase[0] ) ).toEqual( testCase[1] );
});
});
array.forEach( testCases, function( testCase ) {
it( 'double regularizing works for '+testCase[1], function() {
expect( b.regularizeReferenceName( testCase[1] ) ).toEqual( testCase[1] );
});
});
})
});