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