def test_get_genome_data(self): """hg19""" result = GenomicRegionSet("hg19") result.get_genome_data(organism="hg19") self.assertEqual(len(result), 23) """hg19, with Mitochondria chromosome""" result = GenomicRegionSet("hg19") result.get_genome_data(organism="hg19",chrom_M=True) self.assertEqual(len(result), 24)
def test_get_genome_data(self): """hg19""" result = GenomicRegionSet("hg19") result.get_genome_data(organism="hg19") self.assertEqual(len(result), 23) """hg19, with Mitochondria chromosome""" result = GenomicRegionSet("hg19") result.get_genome_data(organism="hg19", chrom_M=True) self.assertEqual(len(result), 24)
args = parser.parse_args() # Setup the entries region = GenomicRegion("sample", initial=0, final=args.l) template = GenomicRegionSet("tamplate") template.add(region) if not os.path.exists(bed_dir): os.makedirs(bed_dir) # Random region result = template.random_regions(organism= "hg19", total_size=args.n, multiply_factor=0, overlap_result=True, overlap_input=True, chrom_X=False, chrom_M=False, filter_path=args.f) result.write(os.path.join(bed_dir, "00total.bed")) chrom = GenomicRegionSet("chrom") chrom.get_genome_data(organism=args.o, chrom_X=False, chrom_M=False) chrom_list = [] for r in chrom.sequences: chrom_list.append(r.chrom) print("Settings:\n\tAllowing overlapping within random regions.") print("Randomizing method:\n\tChoose chromosome with the same possibility (1/23 for each chromosome)\n" + "\tChoose random position with the given length without the regard of previous chosen regions.") print("The distribution of the results are:") for c in chrom_list: print("\t"+str(len(result.any_chrom(c)))+" random regions on " + c) # Write the bed file indivdually