def test_add_track(self):
new_track_name, new_track_file = self.new_track
# Open new track
genome = Genome(self.gdfilepath, mode="r+")
with genome:
self.assertEqual(genome.num_tracks_continuous, 0)
genome.add_track_continuous(new_track_name)
# Load data for new track
load_data(self.gdfilepath, new_track_name,
test_filename(new_track_file), verbose=self.verbose)
# Close data with new track
close_data(self.gdfilepath, verbose=self.verbose)
# Make sure addition was successful
genome = Genome(self.gdfilepath)
with genome:
# Track ordering should now end with dnase
self.assertEqual(genome.tracknames_continuous, [new_track_name])
# Given track ordering, check single track data retrieval
self.assertArraysEqual(genome["chr1"][305:310, new_track_name],
[-2.65300012, 0.37200001, 0.37200001,
0.37200001, 0.37099999])
def test_add_track(self):
new_track_name, new_track_file = self.new_track
# Open new track
genome = Genome(self.gdfilepath, mode="r+")
with warnings.catch_warnings():
warnings.simplefilter("ignore", GenomedataDirtyWarning)
with genome:
self.assertEqual(genome.num_tracks_continuous, 0)
genome.add_track_continuous(new_track_name)
# Load data for new track
load_data(self.gdfilepath,
new_track_name,
test_filename(new_track_file),
verbose=self.verbose)
# Close data with new track
close_data(self.gdfilepath, verbose=self.verbose)
# Make sure addition was successful
genome = Genome(self.gdfilepath)
with genome:
# Track ordering should now end with dnase
self.assertEqual(genome.tracknames_continuous, [new_track_name])
# Given track ordering, check single track data retrieval
self.assertArraysEqual(
genome["chr1"][305:310, new_track_name],
[-2.65300012, 0.37200001, 0.37200001, 0.37200001, 0.37099999])
def test_replace_track(self):
# Test ability to delete and replace a track
old_trackname = "primate"
old_entry = (290, -2.327)
new_trackname = "placental"
new_entry = (290, -2.297)
# Test value before deleting track
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], old_trackname],
old_entry[1])
# Remove track
erase_data(self.gdfilepath, old_trackname,
verbose=self.verbose)
# Now replace it with the data from a different track
track_index = self.tracknames.index(new_trackname)
datafile = self.trackfiles[track_index]
load_data(self.gdfilepath, new_trackname, datafile,
verbose=self.verbose)
# Re-close data
close_data(self.gdfilepath, verbose=self.verbose)
# Now test that the data matches the new track data
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[new_entry[0], new_trackname],
new_entry[1])
def test_replace_track(self):
# Test ability to delete and replace a track
old_trackname = "primate"
old_entry = (290, -2.327)
new_trackname = "placental"
new_entry = (290, -2.297)
# Test value before deleting track
with warnings.catch_warnings():
warnings.simplefilter("ignore", GenomedataDirtyWarning)
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], old_trackname],
old_entry[1])
# Remove track
erase_data(self.gdfilepath, old_trackname, verbose=self.verbose)
# Now replace it with the data from a different track
track_index = self.tracknames.index(new_trackname)
datafile = self.trackfiles[track_index]
load_data(self.gdfilepath,
new_trackname,
datafile,
verbose=self.verbose)
# Re-close data
close_data(self.gdfilepath, verbose=self.verbose)
# Now test that the data matches the new track data
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[new_entry[0], new_trackname],
new_entry[1])
def test_filter_track(self):
# Add filter track
open_data(self.gdfilepath, [UNFILTERED_TRACKNAME],
verbose=self.verbose)
load_data(self.gdfilepath,
UNFILTERED_TRACKNAME,
test_filename(UNFILTERED_TRACK_FILENAME),
verbose=self.verbose)
close_data(self.gdfilepath, verbose=self.verbose)
# Perform filtering on data
hardmask_data(self.gdfilepath,
test_filename(self.filter), [UNFILTERED_TRACKNAME],
lambda x: x < self.filter_threshold,
verbose=self.verbose)
# Make sure filtering was successful
genome = Genome(self.gdfilepath)
with genome:
self.assertArraysEqual(genome["chr1"][0:4, UNFILTERED_TRACKNAME],
[nan, nan, nan, nan])
self.assertArraysEqual(
genome["chr1"][128:132, UNFILTERED_TRACKNAME],
[nan, nan, 0.5, 0.5])
self.assertArraysEqual(
genome["chr1"][168:172, UNFILTERED_TRACKNAME],
[0.9, 0.9, nan, nan])
self.assertArraysEqual(
genome["chr1"][206:210, UNFILTERED_TRACKNAME],
[nan, nan, nan, nan])
def test_delete_tracks(self):
# Test ability to delete a track
trackname = "primate"
old_entry = (290, -2.327)
# Test value before deleting track
warnings.simplefilter("ignore")
with Genome(self.gdfilepath, "r+") as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], trackname],
old_entry[1])
chromosome._erase_data(trackname)
warnings.resetwarnings()
# Re-close data
close_data(self.gdfilepath, verbose=self.verbose)
# Test value after deleting track
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], trackname],
old_entry[1])
def test_delete_tracks(self):
# Test ability to delete a track
trackname = "primate"
old_entry = (290, -2.327)
new_entry = (290, NAN)
# Test value before deleting track
warnings.simplefilter("ignore")
with Genome(self.gdfilepath, "r+") as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], trackname],
old_entry[1])
chromosome._erase_data(trackname)
warnings.resetwarnings()
# Re-close data
close_data(self.gdfilepath, verbose=self.verbose)
# Test value after deleting track
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[old_entry[0], trackname],
old_entry[1])
def test_interface(self):
original_num_datapoints = 0
if self.write:
mode = "r+"
else:
mode = "r"
# catch_warnings acts as a context manager storing the original warning
# filter and resetting it at the end. All non user warnings should
# still be displayed
with warnings.catch_warnings():
warnings.simplefilter("ignore", GenomedataDirtyWarning)
warnings.simplefilter("ignore", OverlapWarning)
with Genome(self.gdfilepath, mode=mode) as genome:
original_num_datapoints = genome.num_datapoints
self.assertTrue("chr1" in genome)
self.assertFalse("chrZ" in genome)
chromosome = genome["chr1"]
# Test tracknames are as expected
self.assertEqual(sorted(chromosome.tracknames_continuous),
sorted(self.tracknames))
# Test tracknames are consistent
self.assertEqual(sorted(genome.tracknames_continuous),
sorted(chromosome.tracknames_continuous))
# Test chromosome attributes
self.assertEqual(chromosome.start, 0)
self.assertEqual(chromosome.end, 24950)
# Test sequence inside of data range
self.assertEqual(seq2str(chromosome.seq[0:20]),
"taaccctaaccctaacccta")
# Test sequence outside of data range
self.assertEqual(seq2str(chromosome.seq[30000]), "n")
# Track ordering should be: placental, primate, vertebrate
self.assertEqual(chromosome.tracknames_continuous,
self.tracknames)
# Given track ordering, check multi-track data retrieval
self.assertArraysEqual(chromosome[290, 0:3],
[-2.297, -2.327, -2.320])
# test multi-track data retrieval by list
self.assertArraysEqual(
chromosome[290, ["placental", "primate", "vertebrate"]],
chromosome[290, 0:3])
self.assertArraysEqual(
chromosome[290, ["placental", "vertebrate"]],
[-2.297, -2.320])
self.assertArraysEqual(chromosome[290, [0, 2]],
[-2.297, -2.320])
self.assertArraysEqual(chromosome[290, [2, 0]],
[-2.320, -2.297])
self.assertArraysEqual(chromosome[290, array([1, 0])],
[-2.327, -2.297])
# Test filling of unassigned continuous segments
chromosome = genome["chrY"]
# Get first supercontig
for supercontig in chromosome:
break
self.assertArraysEqual(supercontig.continuous[0, 2], nan)
# If we are testing writing to archives
if self.write:
# Test writing scalars to various indexing methods
chromosome = genome["chr1"]
# Test writing scalar to multiple tracks
chromosome[290] = 100.0
# Test writing scalar to tracks by named list
chromosome[291,
["placental", "primate", "vertebrate"]] = 101.0
# Test writing scalar to select tracks by named list
chromosome[292, ["placental", "vertebrate"]] = 102.0
# Test writing scalar to tracks by index
chromosome[293, [0, 2]] = 103.0
chromosome[294, [2, 0]] = 104.0
# Test writing arrays to various indexing methods
# Test writing an array to a single index
chromosome[295] = [105.0, 106.0, 107.0]
# Test writing a subarray to a index subset
chromosome[296,
["placental", "vertebrate"]] = [108.0, 109.0]
# Test removing datapoints by writing NaN
chromosome[297, ["primate"]] = nan
# Test writing around supercontig boundaries
# <Supercontig 'supercontig_0', [0:24950]>
# Test writing outside a supercontig
try:
chromosome[300000] = 110.0
except ValueError:
pass # we expect a value error here
# Test writing overlap across supercontig to no supercontig
try:
chromosome[24900:30000] = 111.0
except ValueError:
pass # we expect a value error here
# Check write output after closing if testing writes
if self.write:
# Close with newly written data
close_data(self.gdfilepath, verbose=self.verbose)
# Read data and verify new data and parameters
with Genome(self.gdfilepath) as genome:
chromosome = genome["chr1"]
self.assertArraysEqual(chromosome[290], [100.0, 100.0, 100.0])
self.assertArraysEqual(chromosome[291], [101.0, 101.0, 101.0])
# L14 in primate wigFix
self.assertArraysEqual(chromosome[292], [102.0, 0.371, 102.0])
self.assertArraysEqual(chromosome[293], [103.0, 0.372, 103.0])
self.assertArraysEqual(chromosome[294], [104.0, 0.372, 104.0])
self.assertArraysEqual(chromosome[295], [105.0, 106.0, 107.0])
self.assertArraysEqual(chromosome[296], [108.0, -2.327, 109.0])
# Check if one datapoint was successfully removed
self.assertArraysEqual(original_num_datapoints, [
genome.num_datapoints[0], genome.num_datapoints[1] + 1,
genome.num_datapoints[2]
])
