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_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_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_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])
