def test_fill_subset(self):
"""
Test filling undefined positions on a subset.
"""
walker = sparse('a', [1, 3, 5, 6, 8, 10])
expected = [('a', 1, 1)] + list(filled('a', 3, 8, [4, 7])) + [('a', 10, 10)]
assert_equal(list(wiggelen.fill(walker, regions={'a': (3, 8)})), expected)
def test_fill_open(self):
"""
Test filling undefined positions.
"""
walker = sparse('a', [3, 5, 6, 8])
expected = list(filled('a', 3, 8, [4, 7]))
assert_equal(list(wiggelen.fill(walker)), expected)
def test_fill_closed(self):
"""
Test filling undefined positions with start and stop.
"""
walker = sparse('a', [3, 5, 6, 8])
expected = list(filled('a', 1, 10, [1, 2, 4, 7, 9, 10]))
assert_equal(list(wiggelen.fill(walker, regions={'a': (1, 10)})), expected)
def find_max(regions, wig):
# find max within a given region. Assumes regions are ordered and non-overlapping
# find max by walking through wig file
# Let's also calculate a new score sum just to be extra sure it's right. The
# old score sum was done during merging regions, so it could have been messed up
regions_with_max = []
start, end, score_sum = regions.pop(0)
max_value = -1
max_position = None
new_score_sum = 0
for chrom, position, value in fill(walk(wig)):
if start <= position and position <= end:
new_score_sum += value
if value >= max_value:
max_value = value
max_position = position
if position >= end and max_value != -1:
# position is past region and max_value has been recorded
region_with_max = (start, end, new_score_sum, max_value,
max_position)
regions_with_max.append(region_with_max)
# grab new region and reset max
if len(regions) == 0: # break when there are no more regions
break
start, end, score_sum = regions.pop(0)
max_value = -1
max_position = None
new_score_sum = 0
return regions_with_max
def test_fill_open(self):
"""
Test filling undefined positions.
"""
walker = sparse('a', [3, 5, 6, 8])
expected = list(filled('a', 3, 8, [4, 7]))
assert_equal(list(wiggelen.fill(walker)), expected)
def test_fill_only_edges(self):
"""
Test filling edges of undefined positions.
"""
walker = sparse('a', [3, 5, 6, 14])
expected = [('a', 3, 3), ('a', 4, None), ('a', 5, 5), ('a', 6, 6),
('a', 7, None), ('a', 13, None), ('a', 14, 14)]
assert_equal(list(wiggelen.fill(walker, only_edges=True)), expected)
def test_fill_closed(self):
"""
Test filling undefined positions with start and stop.
"""
walker = sparse('a', [3, 5, 6, 8])
expected = list(filled('a', 1, 10, [1, 2, 4, 7, 9, 10]))
assert_equal(list(wiggelen.fill(walker, regions={'a': (1, 10)})),
expected)
def read_wig(filename, norm=False):
wig_dict = {position : value for region, position, value in fill(walk(open(filename)))}
if norm:
print "Normalizing..."
wig_median = float(np.median(wig_dict.values()))
wig_norm = {x : wig_dict[x]/wig_median for x in wig_dict}
return wig_norm
else:
return wig_dict
def test_fill_subset(self):
"""
Test filling undefined positions on a subset.
"""
walker = sparse('a', [1, 3, 5, 6, 8, 10])
expected = [('a', 1, 1)] + list(filled('a', 3, 8,
[4, 7])) + [('a', 10, 10)]
assert_equal(list(wiggelen.fill(walker, regions={'a': (3, 8)})),
expected)
def main(infile, threshold, merge_dist, min_width, strand, outfile):
# list of tuples, (start, end, avg_exp)
called_regions = []
start = None
end = None
total_exp = 0
# fill function steps through every position, returns None if position not
# in original wig file
print("Calling preliminary regions...")
wig = open(infile)
for region, position, value in fill(walk(wig)):
if start is None:
# initialize start of new region to current position
start = position
if value is None:
if total_exp > 0: # if a region already exists, end it
called_regions.append((start, end, total_exp))
# reset start, end, and total_exp
start = None
end = None
total_exp = 0
elif value < threshold:
if total_exp > 0: # if a region already exists, end it
called_regions.append((start, end, total_exp))
# reset start, end, and total_exp
start = None
end = None
total_exp = 0
elif value >= threshold: # value exceeds threshold, continue region
total_exp += value
end = position
wig.close()
if total_exp != 0: # finished iterating but one last region
called_regions.append((start, end, total_exp))
print("Filtering out regions smaller than minimum width...")
# filter out regions that are below minimum width
filtered_regions = [
x for x in called_regions if x[1] - x[0] + 1 >= min_width
]
print("Merging regions...")
merged_regions = merge_regions(filtered_regions, merge_dist)
# find max region and re-do score sum
# open wig file again
print("Finding region max and calculating total score...")
regions_with_max = find_max(merged_regions, open(infile))
write_bed(regions_with_max, strand, outfile)
def test_fill_only_edges(self):
"""
Test filling edges of undefined positions.
"""
walker = sparse('a', [3, 5, 6, 14])
expected = [('a', 3, 3),
('a', 4, None),
('a', 5, 5),
('a', 6, 6),
('a', 7, None),
('a', 13, None),
('a', 14, 14)]
assert_equal(list(wiggelen.fill(walker, only_edges=True)), expected)
def test_fill_regions(self):
"""
Test filling undefined positions over multiple regions.
"""
a = sparse('a', [3, 5, 6, 8])
b = sparse('b', [3, 5, 6, 8])
c = sparse('c', [1, 3, 5, 6, 8, 10])
walker = chain(a, b, c)
e_a = list(sparse('a', [3, 5, 6, 8]))
e_b = list(filled('b', 1, 10, [1, 2, 4, 7, 9, 10]))
e_c = [('c', 1, 1)] + list(filled('c', 3, 8, [4, 7])) + [('c', 10, 10)]
expected = list(chain(e_a, e_b, e_c))
assert_equal(list(wiggelen.fill(walker, regions={'b': (1, 10), 'c': (3, 8)})), expected)
def test_fill_regions(self):
"""
Test filling undefined positions over multiple regions.
"""
a = sparse('a', [3, 5, 6, 8])
b = sparse('b', [3, 5, 6, 8])
c = sparse('c', [1, 3, 5, 6, 8, 10])
walker = chain(a, b, c)
e_a = list(sparse('a', [3, 5, 6, 8]))
e_b = list(filled('b', 1, 10, [1, 2, 4, 7, 9, 10]))
e_c = [('c', 1, 1)] + list(filled('c', 3, 8, [4, 7])) + [('c', 10, 10)]
expected = list(chain(e_a, e_b, e_c))
assert_equal(
list(wiggelen.fill(walker, regions={
'b': (1, 10),
'c': (3, 8)
})), expected)
return wig_sum
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('bed', help='bed file')
parser.add_argument('plus_wig', help='wig file for plus strand')
parser.add_argument('minus_wig', help='wig file for minus strand')
parser.add_argument('output_name', help='name of output file')
args = parser.parse_args()
plus_wig_dict = {
position: value
for region, position, value in fill(walk(open(args.plus_wig)))
}
minus_wig_dict = {
position: value
for region, position, value in fill(walk(open(args.minus_wig)))
}
outfile = open(args.output_name, 'w')
with open(args.bed) as infile:
for line in infile:
fields = line.strip().split()
chrom = fields[0]
start = int(fields[1])
end = int(fields[2])
name = fields[3]
