def test_gene_annotations():
runner = clt.CliRunner()
input_file = op.join(testdir, 'sample_data', 'exon_unions_mm10.bed')
f = tempfile.NamedTemporaryFile(delete=False)
result = runner.invoke(
cca.bedfile,
[input_file,
'--max-per-tile', '20', '--importance-column', '5',
'--delimiter', '\t',
'--assembly', 'mm10', '--output-file', f.name])
# import traceback
a, b, tb = result.exc_info
'''
print("exc_info:", result.exc_info)
print("result:", result)
print("result.output", result.output)
print("result.error", traceback.print_tb(tb))
print("Exception:", a,b)
'''
rows = cdt.get_tiles(f.name, 0, 0)
assert(len(rows[0]) == 2)
rows = cdt.get_tiles(f.name, 11, 113)
assert(rows[113][0]['fields'][3] == 'Lrp1b')
rows = cdt.get_tiles(f.name, 11, 112)
assert(rows[112][0]['fields'][3] == 'Lrp1b')
def test_clodius_aggregate_bedfile():
input_file = op.join(testdir, 'sample_data',
'geneAnnotationsExonsUnions.hg19.short.bed')
output_file = '/tmp/geneAnnotationsExonsUnions.hg19.short.bed'
runner = clt.CliRunner()
result = runner.invoke(cca.bedfile, [
input_file, '--max-per-tile', 20, '--importance-column', 5,
'--assembly', 'hg19', '--output-file', output_file, '--delimiter', '\t'
])
print("exc_info:", result.exc_info)
a, b, tb = result.exc_info
print("result:", result)
print("result.output", result.output)
print("result.error", traceback.print_tb(tb))
print("Exception:", a, b)
assert (result.exit_code == 0)
results = cdt.get_tiles(output_file, 6, 3, num_tiles=1)
print("results:", results)
assert (len(results[3][0]['fields']) == 14)
runner = clt.CliRunner()
result = runner.invoke(cca.bedfile, [
input_file, '--max-per-tile', 20, '--importance-column', 5,
'--assembly', 'hg19', '--output-file', output_file
])
assert (result.exit_code == 0)
results = cdt.get_tiles(output_file, 6, 3, num_tiles=3)
assert (len(results[3][0]['fields']) == 17)
def test_clodius_aggregate_bedfile():
input_file = op.join(testdir, "sample_data",
"geneAnnotationsExonsUnions.hg19.short.bed")
output_file = "/tmp/geneAnnotationsExonsUnions.hg19.short.bed"
runner = clt.CliRunner()
result = runner.invoke(
cca.bedfile,
[
input_file,
"--max-per-tile",
20,
"--importance-column",
5,
"--assembly",
"hg19",
"--output-file",
output_file,
"--delimiter",
"\t",
],
)
a, b, tb = result.exc_info
"""
print("exc_info:", result.exc_info)
print("result:", result)
print("result.output", result.output)
print("result.error", traceback.print_tb(tb))
print("Exception:", a,b)
"""
assert result.exit_code == 0
results = cdt.get_tiles(output_file, 6, 3, num_tiles=1)
# print("results:", results)
assert len(results[3][0]["fields"]) == 14
runner = clt.CliRunner()
result = runner.invoke(
cca.bedfile,
[
input_file,
"--max-per-tile",
20,
"--importance-column",
5,
"--assembly",
"hg19",
"--output-file",
output_file,
],
)
assert result.exit_code == 0
results = cdt.get_tiles(output_file, 6, 3, num_tiles=3)
assert len(results[3][0]["fields"]) == 17
def test_random_importance():
# check that when aggregating using random importance, all values that
# are in a higher resolution tile are also in the lower resolution
f = tempfile.NamedTemporaryFile(delete=False)
runner = clt.CliRunner()
input_file = op.join(testdir, 'sample_data', '25435_PM15-000877_SM-7QK6O.seg')
result = runner.invoke(
cca.bedfile,
[input_file,
'--max-per-tile', '2', '--importance-column', 'random',
'--assembly', 'b37', '--has-header', '--output-file', f.name])
import traceback
print("exc_info:", result.exc_info)
a,b,tb = result.exc_info
print("result:", result)
print("result.output", result.output)
print("result.error", traceback.print_tb(tb))
print("Exception:", a,b)
tileset_info = cdt.get_tileset_info(f.name)
# print("tileset_info:", tileset_info)
rows = cdt.get_tiles(f.name, 0, 0)
#print("rows:", rows)
rows = list(cdt.get_tiles(f.name, 1, 0).values()) + list(cdt.get_tiles(f.name, 1,1).values())
#print('rows:', rows)
found = False
for row in cdt.get_tiles(f.name, 6, 31).values():
for rect in row:
if rect['xEnd'] == 2195875458:
found = True
found = False
for row in cdt.get_tiles(f.name, 6, 32).values():
for rect in row:
if rect['xEnd'] == 2195875458:
found = True
assert(found == True)
pass
def test_get_tiles():
filename = 'test/sample_data/gene_annotations.short.db'
tiles = cdt.get_tiles(filename, 18, 169283)[169283]
# print("tiles:", tiles)
x = int(tiles[0]['xStart'])
fields = tiles[0]['fields']
def test_random_importance():
# check that when aggregating using random importance, all values that
# are in a higher resolution tile are also in the lower resolution
f = tempfile.NamedTemporaryFile(delete=False)
runner = clt.CliRunner()
input_file = op.join(testdir, 'sample_data',
'25435_PM15-000877_SM-7QK6O.seg')
result = runner.invoke(
cca.bedfile,
[input_file,
'--max-per-tile', '2', '--importance-column', 'random',
'--assembly', 'b37', '--has-header', '--output-file', f.name])
# import traceback
a, b, tb = result.exc_info
'''
print("exc_info:", result.exc_info)
print("result:", result)
print("result.output", result.output)
print("result.error", traceback.print_tb(tb))
print("Exception:", a,b)
'''
cdt.get_tileset_info(f.name)
# print("tileset_info:", tileset_info)
# TODO: Make assertions about result
cdt.get_tiles(f.name, 0, 0)
# print("rows:", rows)
# TODO: Make assertions about result
list(cdt.get_tiles(f.name, 1, 0).values()) + \
list(cdt.get_tiles(f.name, 1, 1).values())
# print('rows:', rows)
# TODO: Make assertions about result
# check to make sure that tiles in the higher zoom levels
# are all present in lower zoom levels
found = {}
for row in cdt.get_tiles(f.name, 5, 15).values():
for rect in row:
found[rect['xStart']] = False
for row in cdt.get_tiles(f.name, 6, 30).values():
for rect in row:
if rect['xStart'] in found:
found[rect['xStart']] = True
for row in cdt.get_tiles(f.name, 6, 31).values():
for rect in row:
if rect['xStart'] in found:
found[rect['xStart']] = True
for key, value in found.items():
assert(value)
pass
def generate_beddb_tiles(tileset, tile_ids):
'''
Generate tiles from a beddb file.
Parameters
----------
tileset: tilesets.models.Tileset object
The tileset that the tile ids should be retrieved from
tile_ids: [str,...]
A list of tile_ids (e.g. xyx.0.1) identifying the tiles
to be retrieved
Returns
-------
generated_tiles: [(tile_id, tile_data),...]
A list of tile_id, tile_data tuples
'''
tile_ids_by_zoom = bin_tiles_by_zoom(tile_ids).values()
partitioned_tile_ids = list(it.chain(*[partition_by_adjacent_tiles(t, dimension=1)
for t in tile_ids_by_zoom]))
generated_tiles = []
for tile_group in partitioned_tile_ids:
zoom_level = int(tile_group[0].split('.')[1])
tileset_id = tile_group[0].split('.')[0]
tile_positions = [[int(x) for x in t.split('.')[2:3]] for t in tile_group]
if len(tile_positions) == 0:
continue
minx = min([t[0] for t in tile_positions])
maxx = max([t[0] for t in tile_positions])
t1 = time.time()
tile_data_by_position = cdt.get_tiles(
get_cached_datapath(tileset.datafile.url),
zoom_level,
minx,
maxx - minx + 1
)
generated_tiles += [(".".join(map(str, [tileset_id] + [zoom_level] + [position])), tile_data)
for (position, tile_data) in tile_data_by_position.items()]
return generated_tiles
def test_chromosome_limit():
f = tempfile.NamedTemporaryFile(delete=False)
runner = clt.CliRunner()
input_file = op.join(testdir, 'sample_data',
'geneAnnotationsExonsUnions.short.bed')
result = runner.invoke(cca.bedfile, [
input_file, '--max-per-tile', '60', '--importance-column', '5',
'--assembly', 'hg19', '--chromosome', 'chr14', '--output-file', f.name
])
# print('output:', result.output, result)
rows = cdt.get_tiles(f.name, 0, 0)[0]
foundOther = False
for row in rows:
assert (row['fields'][0] == 'chr14')
os.remove(f.name)
pass
def test_no_chromosome_limit():
f = tempfile.NamedTemporaryFile(delete=False)
runner = clt.CliRunner()
input_file = op.join(testdir, 'sample_data',
'geneAnnotationsExonsUnions.short.bed')
result = runner.invoke(
cca.bedfile,
[input_file,
'--max-per-tile', '60', '--importance-column', '5',
'--assembly', 'hg19',
'--output-file', f.name])
# import traceback
'''
print("exc_info:", result.exc_info)
print("result:", result)
print("result.output", result.output)
print("result.error", traceback.print_tb(tb))
print("Exception:", a,b)
'''
a, b, tb = result.exc_info
rows = cdt.get_tiles(f.name, 0, 0)[0]
foundOther = False
for row in rows:
if row['fields'][0] != 'chr1':
# print("row", row)
assert(row['xStart'] > 200000000)
if row['fields'][0] != 'chr14':
foundOther = True
break
# make sure there's chromosome other than 14 in the output
assert(foundOther)
os.remove(f.name)
pass
def test_get_tiles():
filename = 'test/sample_data/gene_annotations.short.db'
cdt.get_tiles(filename, 18, 169283)[169283]
