def test_junction_extraction_from_splitmap(): input = files.open(testfiles["reads_1.fastq"]) index = testfiles["genome.gem"] gtf_junctions = set(junctions.from_gtf(testfiles["refseq.gtf"])) jj = gem.extract_junctions(input, index, merge_with=gtf_junctions) assert junctions is not None assert len(jj) == 260
def test_junction_extraction_from_gtf(): gtf_junctions = list(junctions.from_gtf(testfiles["refseq.gtf"])) assert len(gtf_junctions) == 260 junctions.write_junctions(gtf_junctions, results_dir + "/annotation.junctions") ## reread the junctions reread = junctions.from_junctions(results_dir + "/annotation.junctions") assert reread is not None assert len(reread) == 260 assert len(set(gtf_junctions).intersection(set(reread))) == 260 ## merge junctions merged = junctions.merge_junctions([gtf_junctions, reread]) assert merged is not None assert len(merged) == 260