def create_trees_dict(intervals_file):
"""
Create a dictionary in which each key is a chromosome and its value is an
interval tree containing all the intervals in that chromosome.
"""
# Temp dictionary that holds a list of all the intervals in each chromosme.
chromosomes = defaultdict(list)
with open(intervals_file) as fin:
slines = (line.rstrip().split(None, 3) for line in fin)
for inter in slines:
try:
interval = [int(inter[1]), int(inter[2])]
# Check that the input file is in BED format.
except IndexError:
raise InputFormatError('Tree file must be in BED format.')
except ValueError:
raise InputFormatError('Tree file must be in BED format.')
if len(inter) > 3:
interval.append(inter[3])
interval = tuple(interval)
chromosomes[inter[0]].append(interval)
# Final dictionary with one tree per chromosome.
trees = defaultdict()
for chromosome in chromosomes:
trees[chromosome] = build_tree(sorted(chromosomes[chromosome]))
del chromosomes
return trees
def create_trees_dict(intervals_file):
"""
Create a dictionary in which each key is a chromosome and its value is an
interval tree containing all the intervals in that chromosome.
"""
# Temp dictionary that holds a list of all the intervals in each chromosme.
chromosomes = defaultdict(list)
with open(intervals_file) as fin:
slines = (line.rstrip().split(None, 3) for line in fin)
for inter in slines:
try:
interval = [int(inter[1]), int(inter[2])]
# Check that the input file is in BED format.
except IndexError:
raise InputFormatError("Tree file must be in BED format.")
except ValueError:
raise InputFormatError("Tree file must be in BED format.")
if len(inter) > 3:
interval.append(inter[3])
interval = tuple(interval)
chromosomes[inter[0]].append(interval)
# Final dictionary with one tree per chromosome.
trees = defaultdict()
for chromosome in chromosomes:
trees[chromosome] = build_tree(sorted(chromosomes[chromosome]))
del chromosomes
return trees
raise InputFormatError('Query file must be in BED format.')
except ValueError:
raise InputFormatError('Query file must be in BED format.')
if len(interval) > 2:
try:
query.append(int(interval[2]))
except ValueError:
raise InputFormatError('Query file must be in BED format.')
query = tuple(query)
for overlap in find_overlaps(trees, query):
print '\t'.join(str(i) for i in overlap)
if __name__ == '__main__':
try:
tree_file = sys.argv[1]
query_file = sys.argv[2]
trees = create_trees_dict(tree_file)
with open(query_file) as quf:
slines = (line.rstrip().split(None, 3) for line in quf)
for sl in slines:
_query_from_main(trees, sl)
except IndexError:
print('Please use the following format:\n' +
'ting.py <tree_file> <query_file>')
except IndexError:
raise InputFormatError("Query file must be in BED format.")
except ValueError:
raise InputFormatError("Query file must be in BED format.")
if len(interval) > 2:
try:
query.append(int(interval[2]))
except ValueError:
raise InputFormatError("Query file must be in BED format.")
query = tuple(query)
for overlap in find_overlaps(trees, query):
print "\t".join(str(i) for i in overlap)
if __name__ == "__main__":
try:
tree_file = sys.argv[1]
query_file = sys.argv[2]
trees = create_trees_dict(tree_file)
with open(query_file) as quf:
slines = (line.rstrip().split(None, 3) for line in quf)
for sl in slines:
_query_from_main(trees, sl)
except IndexError:
print ("Please use the following format:\n" + "ting.py <tree_file> <query_file>")
