def check_random_windows_against_wig(self, strand):
chrdict = self.chrdict
chroms = list(self.chrdict)
chridx = numpy.random.randint(0, high=len(chroms), size=50)
ga = GenomeArray()
i = 0
with open(wigfile) as fin:
ga.add_from_wiggle(fin, strand)
while i < 50:
chrom = chroms[chridx[i]]
maxlength = chrdict[chrom]
start = numpy.random.randint(0, high=maxlength - 2000)
end = numpy.random.randint(start + 10000, high=start + 20000)
# make sure we don't go off chrom
while end > maxlength:
end = numpy.random.randint(start + 100, high=start + 10000)
seg = GenomicSegment(chrom, start, end, strand)
expected = ga[seg]
# make sure segment has counts in it
if expected.sum() > 0:
i += 1
found = self.bw[seg]
yield self.check_vals_against_wig, expected, found
def check_random_windows_against_wig(self, strand):
chrdict = self.chrdict
chroms = list(self.chrdict)
chridx = numpy.random.randint(0, high=len(chroms), size=50)
ga = GenomeArray()
i = 0
with open(wigfile) as fin:
ga.add_from_wiggle(fin, strand)
while i < 50:
chrom = chroms[chridx[i]]
maxlength = chrdict[chrom]
start = numpy.random.randint(0, high=maxlength - 2000)
end = numpy.random.randint(start + 10000, high=start + 20000)
# make sure we don't go off chrom
while end > maxlength:
end = numpy.random.randint(start + 100, high=start + 10000)
seg = GenomicSegment(chrom, start, end, strand)
expected = ga[seg]
# make sure segment has counts in it
if expected.sum() > 0:
i += 1
found = self.bw[seg]
yield self.check_vals_against_wig, expected, found
def test_get_chromosome_counts_zero_fill(self):
ga = GenomeArray()
with open(wigfile) as fin:
ga.add_from_wiggle(fin, "+")
for chrom, length in self.chrdict.items():
seg = GenomicSegment(chrom, 0, length, "+")
expected = ga[seg]
found = self.bw.get_chromosome_counts(chrom)
yield self.check_vals_against_wig, expected, found
def test_get_chromosome_counts_zero_fill(self):
ga = GenomeArray()
with open(wigfile) as fin:
ga.add_from_wiggle(fin, "+")
for chrom, length in self.chrdict.items():
seg = GenomicSegment(chrom, 0, length, "+")
expected = ga[seg]
found = self.bw.get_chromosome_counts(chrom)
yield self.check_vals_against_wig, expected, found
def do_check(argstr, ref_files, test_files):
"""Check that test wiggle files match reference files
Parameters
----------
ref_files : tuple
Tuple of filenames corresponding to forward and reverse strand wiggles
for reference dataset
test_files : list
Tuple of filenames corresponding to forward and reverse strand wiggles
for test dataset
"""
err_message = "Unequal output in files %s vs %s, module %s" % (
ref_files, test_files, test_info["module_name"])
test_info["test_method"](shlex.split(argstr))
ref_ga = GenomeArray()
test_ga = GenomeArray()
ref_ga.add_from_wiggle(open(ref_files[0]), "+")
ref_ga.add_from_wiggle(open(ref_files[1]), "-")
test_ga.add_from_wiggle(open(test_files[0]), "+")
test_ga.add_from_wiggle(open(test_files[1]), "-")
nose.tools.assert_true(ref_ga.__eq__(test_ga, tol=1e-8), err_message)
def do_check(argstr,ref_files,test_files):
"""Check that test wiggle files match reference files
Parameters
----------
ref_files : tuple
Tuple of filenames corresponding to forward and reverse strand wiggles
for reference dataset
test_files : list
Tuple of filenames corresponding to forward and reverse strand wiggles
for test dataset
"""
err_message = "Unequal output in files %s vs %s, module %s" % (ref_files,test_files,test_info["module_name"])
test_info["test_method"](shlex.split(argstr))
ref_ga = GenomeArray()
test_ga = GenomeArray()
ref_ga.add_from_wiggle(open(ref_files[0]),"+")
ref_ga.add_from_wiggle(open(ref_files[1]),"-")
test_ga.add_from_wiggle(open(test_files[0]),"+")
test_ga.add_from_wiggle(open(test_files[1]),"-")
nose.tools.assert_true(ref_ga.__eq__(test_ga,tol=1e-8),err_message)