def test_target(self):
"""The 'target' command."""
annot_fname = "formats/refflat-mini.txt"
for bait_fname in ("formats/nv2_baits.interval_list",
"formats/amplicon.bed"):
baits = tabio.read_auto(bait_fname)
bait_len = len(baits)
# No splitting: w/ and w/o re-annotation
r1 = commands.do_target(baits)
self.assertEqual(len(r1), bait_len)
r1a = commands.do_target(baits,
do_short_names=True,
annotate=annot_fname)
self.assertEqual(len(r1a), len(r1))
# Splitting
r2 = commands.do_target(baits,
do_short_names=True,
do_split=True,
avg_size=100)
self.assertGreater(len(r2), len(r1))
r2a = commands.do_target(baits,
do_short_names=True,
do_split=True,
avg_size=100,
annotate=annot_fname)
self.assertEqual(len(r2a), len(r2))
# Original regions object should be unmodified
self.assertEqual(len(baits), bait_len)
def test_target(self):
"""The 'target' command."""
#return # DBG
annot_fname = "formats/refflat-mini.txt"
for bait_fname in ("formats/nv2_baits.interval_list",
"formats/amplicon.bed",
"formats/baits-funky.bed"):
baits = tabio.read_auto(bait_fname)
bait_len = len(baits)
# No splitting: w/o and w/ re-annotation
r1 = commands.do_target(baits)
self.assertEqual(len(r1), bait_len)
r1a = commands.do_target(baits, do_short_names=True,
annotate=annot_fname)
self.assertEqual(len(r1a), len(r1))
# Splitting, w/o and w/ re-annotation
r2 = commands.do_target(baits, do_short_names=True, do_split=True,
avg_size=100)
self.assertGreater(len(r2), len(r1))
for _c, subarr in r2.by_chromosome():
self.assertTrue(subarr.start.is_monotonic_increasing, bait_fname)
self.assertTrue(subarr.end.is_monotonic_increasing, bait_fname)
# Bins are non-overlapping; next start >= prev. end
self.assertTrue(
((subarr.start.values[1:] - subarr.end.values[:-1])
>= 0).all())
r2a = commands.do_target(baits, do_short_names=True, do_split=True,
avg_size=100, annotate=annot_fname)
self.assertEqual(len(r2a), len(r2))
# Original regions object should be unmodified
self.assertEqual(len(baits), bait_len)
def test_target(self):
"""The 'target' command."""
annot_fname = "formats/refflat-mini.txt"
for bait_fname in ("formats/nv2_baits.interval_list",
"formats/amplicon.bed"):
baits = tabio.read_auto(bait_fname)
bait_len = len(baits)
# No splitting: w/ and w/o re-annotation
r1 = commands.do_target(baits)
self.assertEqual(len(r1), bait_len)
r1a = commands.do_target(baits, do_short_names=True,
annotate=annot_fname)
self.assertEqual(len(r1a), len(r1))
# Splitting
r2 = commands.do_target(baits, do_short_names=True, do_split=True,
avg_size=100)
self.assertGreater(len(r2), len(r1))
r2a = commands.do_target(baits, do_short_names=True, do_split=True,
avg_size=100, annotate=annot_fname)
self.assertEqual(len(r2a), len(r2))
# Original regions object should be unmodified
self.assertEqual(len(baits), bait_len)
def test_target(self):
"""The 'target' command."""
#return # DBG
annot_fname = "formats/refflat-mini.txt"
for bait_fname in ("formats/nv2_baits.interval_list",
"formats/amplicon.bed", "formats/baits-funky.bed"):
baits = tabio.read_auto(bait_fname)
bait_len = len(baits)
# No splitting: w/o and w/ re-annotation
r1 = commands.do_target(baits)
self.assertEqual(len(r1), bait_len)
r1a = commands.do_target(baits,
do_short_names=True,
annotate=annot_fname)
self.assertEqual(len(r1a), len(r1))
# Splitting, w/o and w/ re-annotation
r2 = commands.do_target(baits,
do_short_names=True,
do_split=True,
avg_size=100)
self.assertGreater(len(r2), len(r1))
for _c, subarr in r2.by_chromosome():
self.assertTrue(subarr.start.is_monotonic_increasing,
bait_fname)
self.assertTrue(subarr.end.is_monotonic_increasing, bait_fname)
# Bins are non-overlapping; next start >= prev. end
self.assertTrue(
((subarr.start.values[1:] - subarr.end.values[:-1]) >=
0).all())
r2a = commands.do_target(baits,
do_short_names=True,
do_split=True,
avg_size=100,
annotate=annot_fname)
self.assertEqual(len(r2a), len(r2))
# Original regions object should be unmodified
self.assertEqual(len(baits), bait_len)