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import pytest
import sys
import os
import glob
import sysconfig
from pathlib import Path
import unittest
import pytest
import conftest
build_dir = "build/lib.%s-%s" % (sysconfig.get_platform(), sys.version[0:3])
sys.path.insert(0, os.path.join(os.getcwd(), build_dir))
import HTSeq
try:
import pyBigWig
except ImportError:
pyBigWig = None
data_folder = conftest.get_data_folder()
class TestGenomicInterval(unittest.TestCase):
def test_init(self):
iv = HTSeq.GenomicInterval(
'chr1', 100, 200, ".",
)
class TestChromVector(unittest.TestCase):
def test_init_step(self):
# Autoallocation
cv = HTSeq.ChromVector.create(
HTSeq.GenomicInterval('chr1', 100, 200, "."),
typecode='d',
storage='step',
)
def test_init_stretch(self):
# Autoallocation
cv = HTSeq.ChromVector.create(
HTSeq.GenomicInterval('chr1', 100, 200, "."),
typecode='d',
storage='stretch',
)
def test_steps_stretch(self):
cv = HTSeq.ChromVector.create(
HTSeq.GenomicInterval('chr1', 100, 200, "."),
typecode='d',
storage='stretch',
)
cv[120:130] = 45
cv[129:140] = 89
cv[180: 182] = 1
steps = list(cv.steps())
self.assertEqual(steps[0][0], HTSeq.GenomicInterval('chr1', 120, 129))
self.assertEqual(steps[1][0], HTSeq.GenomicInterval('chr1', 129, 140))
self.assertEqual(steps[2][0], HTSeq.GenomicInterval('chr1', 180, 182))
self.assertEqual(steps[0][1], 45)
self.assertEqual(steps[1][1], 89)
self.assertEqual(steps[2][1], 1)
class TestGenomicArray(unittest.TestCase):
def test_init(self):
# Autoallocation
ga = HTSeq.GenomicArray("auto")
# Infinite length chromosomes
ga = HTSeq.GenomicArray(['1', '2'])
# Fixed chromosomes
ga = HTSeq.GenomicArray({
'1': 5898,
'2': 4876,
})
# Store: ndarray
ga = HTSeq.GenomicArray({
'1': 5898,
'2': 4876,
},
storage='ndarray',
)
# Store: memmap
ga = HTSeq.GenomicArray({
'1': 5898,
'2': 4876,
},
storage='memmap',
memmap_dir='.',
)
def test_steps(self):
for storage in ['step', 'ndarray']:
ga = HTSeq.GenomicArray({
'1': 5898,
'2': 4876,
},
storage=storage,
)
steps = ga.steps()
steps_exp = [
(HTSeq.GenomicInterval('1', 0, 5898, strand='+'), 0),
(HTSeq.GenomicInterval('1', 0, 5898, strand='-'), 0),
(HTSeq.GenomicInterval('2', 0, 4876, strand='+'), 0),
(HTSeq.GenomicInterval('2', 0, 4876, strand='-'), 0),
]
for step, step_exp in zip(steps, steps_exp):
self.assertEqual(step, step_exp)
def test_access_out_of_range(self):
""" Ensure chromosomes are made with infinite size, which can be accessed """
def _get_arrays():
return {
"Provided chrom": HTSeq.GenomicArray(["1"], typecode='O'),
"Auto chrom": HTSeq.GenomicArray("auto", typecode='O'),
}
# Test we can access unknown regions without error
unknown_iv = HTSeq.GenomicInterval('1', 200, 300, "+")
for name, genomic_array in _get_arrays().items():
step = list(genomic_array[unknown_iv].steps())[0]
unknown_value = step[1]
self.assertIsNone(unknown_value, msg="Access unknown in " + name)
# Test accessing unknown regions works the same even if we call setter first
known_iv = HTSeq.GenomicInterval('1', 0, 100, strand='+')
for name, genomic_array in _get_arrays().items():
# Call setter first before getter
genomic_array[known_iv] = "test"
step = list(genomic_array[unknown_iv].steps())[0]
unknown_value = step[1]
self.assertIsNone(unknown_value, msg="Access unknown after calling setter in " + name)
def test_bedgraph(self):
def compare_bedgraph_line(line1, line2):
fields1 = line1.split()
fields2 = line2.split()
# Chromosome
self.assertEqual(fields1[0], fields2[0])
# Start-end
self.assertEqual(int(fields1[1]), int(fields2[1]))
self.assertEqual(int(fields1[2]), int(fields2[2]))
# Value
self.assertEqual(float(fields1[3]), float(fields2[3]))
ga = HTSeq.GenomicArray.from_bedgraph_file(
data_folder+'example_bedgraph.bedgraph',
strand='.',
)
steps = []
for iv, value in ga.steps():
steps.append((iv.chrom, iv.start, iv.end, value))
steps_exp = [
('chr19', 49302000, 49302300, -1.0),
('chr19', 49302300, 49302600, -0.75),
('chr19', 49302600, 49302900, -0.50),
('chr19', 49302900, 49303200, -0.25),
('chr19', 49303200, 49303500, 0.0),
('chr19', 49303500, 49303800, 0.25),
('chr19', 49303800, 49304100, 0.50),
('chr19', 49304100, 49304400, 0.75),
('chr19', 49304400, 49304700, 1.00),
]
self.assertEqual(steps, steps_exp)
ga.write_bedgraph_file(
'test_output.bedgraph',
track_options='name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20',
separator=' ',
)
with open(data_folder+'example_bedgraph.bedgraph') as f1, \
open('test_output.bedgraph') as f2:
header_found = False
for line1, line2 in zip(f1, f2):
if not header_found:
self.assertEqual(line1, line2)
else:
compare_bedgraph_line(line1, line2)
if 'track type' in line1:
header_found = True
@unittest.skipIf(pyBigWig is None, "test case depends on pyBigWig")
def test_bigwig(self):
ga = HTSeq.GenomicArray.from_bigwig_file(
data_folder+'example_bigwig.bw',
)
ga.write_bigwig_file(
'test_output.bw',
)
import pyBigWig
with pyBigWig.open(data_folder+'example_bigwig.bw') as bw1, \
pyBigWig.open('test_output.bw') as bw2:
self.assertEqual(bw1.chroms(), bw2.chroms())
for chrom in bw1.chroms():
self.assertEqual(
bw1.intervals(chrom),
bw2.intervals(chrom),
)
def test_access_out_of_range(self):
""" Ensure chromosomes are made with infinite size, which can be accessed """
def _get_arrays():
return {
"Provided chrom": HTSeq.GenomicArray(["1"], typecode='O'),
"Auto chrom": HTSeq.GenomicArray("auto", typecode='O'),
}
# Test we can access unknown regions without error
unknown_iv = HTSeq.GenomicInterval('1', 200, 300, "+")
for name, genomic_array in _get_arrays().items():
step = list(genomic_array[unknown_iv].steps())[0]
unknown_value = step[1]
self.assertIsNone(unknown_value, msg="Access unknown in " + name)
# Test accessing unknown regions works the same even if we call setter first
known_iv = HTSeq.GenomicInterval('1', 0, 100, strand='+')
for name, genomic_array in _get_arrays().items():
# Call setter first before getter
genomic_array[known_iv] = "test"
step = list(genomic_array[unknown_iv].steps())[0]
unknown_value = step[1]
self.assertIsNone(unknown_value, msg="Access unknown after calling setter in " + name)
if __name__ == '__main__':
suite = TestGenomicArray()
suite.test_init()
|
