def test_read_splice_sites(exon2_bed, direction, simulated_fasta, simulated_chromsizes, negative_control_folder): from outrigger.validate.check_splice_sites import read_splice_sites test = read_splice_sites(exon2_bed, simulated_chromsizes, simulated_fasta, direction) csv = os.path.join(negative_control_folder, 'exon2_{}_splice_sites.csv'.format(direction)) true = pd.read_csv(csv, index_col=0, squeeze=True, header=None, names=None) true.name = None true.index.name = None pdt.assert_series_equal(test, true)
def individual_exon_splice_sites(self, exon, splice_abbrev, direction): exon_bed = os.path.join(self.input_index, splice_abbrev, '{}.bed'.format(exon)) splice_sites = check_splice_sites.read_splice_sites( exon_bed, self.genome, self.fasta, direction) return splice_sites