def test_clodius_aggregate_bedpe():
input_file = op.join(testdir, "sample_data", "isidro.bedpe")
with tempfile.TemporaryDirectory() as tmpdirname:
output_file = op.join(tmpdirname, "isidro.bed2ddb")
cca._bedpe(
input_file,
output_file,
"b37",
importance_column=None,
chromosome=None,
max_per_tile=100,
tile_size=1024,
has_header=True,
)
"""
runner = clt.CliRunner()
result = runner.invoke(
cca.bedpe,
[input_file,
'--output-file', output_file,
'--importance-column', 'random',
'--has-header',
'--assembly', 'b37'])
# print('output:', result.output, result)
assert(result.exit_code == 0)
"""
cdt.get_2d_tiles(output_file, 0, 0, 0)
# print("entries:", entries)
cdt.get_tileset_info(output_file)
# TODO: Make assertions about result
# print('tileset_info', tileset_info)
cdt.get_2d_tiles(output_file, 1, 0, 0, numx=2, numy=2)
# TODO: Make assertions about result
# print("entries:", entries)
cdt.get_tileset_info(output_file)
def test_clodius_aggregate_bedpe():
input_file = op.join(testdir, 'sample_data', 'isidro.bedpe')
output_file = '/tmp/isidro.bed2ddb'
cca._bedpe(input_file,
output_file,
'b37',
importance_column=None,
chromosome=None,
max_per_tile=100,
tile_size=1024,
has_header=True)
"""
runner = clt.CliRunner()
result = runner.invoke(
cca.bedpe,
[input_file,
'--output-file', output_file,
'--importance-column', 'random',
'--has-header',
'--assembly', 'b37'])
#print('output:', result.output, result)
assert(result.exit_code == 0)
"""
entries = cdt.get_2d_tiles(output_file, 0, 0, 0)
#print("entries:", entries)
tileset_info = cdt.get_tileset_info(output_file)
#print('tileset_info', tileset_info)
entries = cdt.get_2d_tiles(output_file, 1, 0, 0, numx=2, numy=2)
#print("entries:", entries)
tileset_info = cdt.get_tileset_info(output_file)
def test_clodius_aggregate_bedpe():
input_file = op.join(testdir, 'sample_data',
'Rao_RepA_GM12878_Arrowhead.txt')
output_file = '/tmp/bedpe.db'
runner = clt.CliRunner()
result = runner.invoke(cca.bedpe, [
input_file, '--output-file', output_file, '--assembly', 'hg19',
'--chr1-col', '1', '--from1-col', '2', '--to1-col', '3', '--chr2-col',
'1', '--from2-col', '2', '--to2-col', '3'
])
print("result:", result)
print("result.output", result.output)
assert (result.exit_code == 0)
tiles = cdt.get_2d_tiles(output_file, 0, 0, 0, numx=1, numy=1)
print("tiles:", tiles)
assert ('\n' not in tiles[(0, 0)][0]['fields'][2])
def test_clodius_aggregate_bedpe():
input_file = op.join(testdir, "sample_data",
"Rao_RepA_GM12878_Arrowhead.txt")
output_file = "/tmp/bedpe.db"
runner = clt.CliRunner()
result = runner.invoke(
cca.bedpe,
[
input_file,
"--output-file",
output_file,
"--assembly",
"hg19",
"--chr1-col",
"1",
"--from1-col",
"2",
"--to1-col",
"3",
"--chr2-col",
"1",
"--from2-col",
"2",
"--to2-col",
"3",
],
)
"""
print("result:", result)
print("result.output", result.output)
"""
assert result.exit_code == 0
tiles = cdt.get_2d_tiles(output_file, 0, 0, 0, numx=1, numy=1)
assert "\n" not in tiles[(0, 0)][0]["fields"][2]
def test_clodius_aggregate_bedpe():
input_file = op.join(testdir, "sample_data",
"Rao_RepA_GM12878_Arrowhead.txt")
output_file = "/tmp/bedpe.db"
# make sure that aggregating without an assembly throws
# doesn't succeed
runner = clt.CliRunner()
result = runner.invoke(
cca.bedpe,
[
input_file,
"--output-file",
output_file,
"--chr1-col",
"1",
"--from1-col",
"2",
"--to1-col",
"3",
"--chr2-col",
"1",
"--from2-col",
"2",
"--to2-col",
"3",
],
)
assert result.exit_code == 1
runner = clt.CliRunner()
result = runner.invoke(
cca.bedpe,
[
input_file,
"--output-file",
output_file,
"--assembly",
"hg19",
"--chr1-col",
"1",
"--from1-col",
"2",
"--to1-col",
"3",
"--chr2-col",
"1",
"--from2-col",
"2",
"--to2-col",
"3",
],
)
"""
print("result:", result)
print("result.output", result.output)
"""
assert result.exit_code == 0
tiles = cdt.get_2d_tiles(output_file, 0, 0, 0, numx=1, numy=1)
assert "\n" not in tiles[(0, 0)][0]["fields"][2]
tiles_2d = bed2ddb.tiles(output_file, ["x.0.0.0"])
assert len(tiles_2d[0][1][0]["fields"]) == 3
tiles_1d = bed2ddb.tiles(output_file, ["x.0.0"])
assert len(tiles_1d[0][1][0]["fields"]) == 3
def test_get_tiles():
filename = "test/sample_data/arrowhead_domains_short.txt.multires.db"
cdt.get_2d_tiles(filename, 0, 0, 0, numx=1, numy=1)
def test_get_tiles():
filename = 'test/sample_data/arrowhead_domains_short.txt.multires.db'
tiles = cdt.get_2d_tiles(filename, 0,0,0, numx=1, numy=1)
print("tiles:", tiles)
