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"""
Support for creating dictionaries of `Bitset`s / `BinnedBitset`s from text
files containg sets of "covered" intervals in sequences (e.g. `BED`_ files).
.. BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
"""
import re
from warnings import warn
from bx.bitset import (
BinnedBitSet,
MAX,
)
def binned_bitsets_from_file(
f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream_pad=0, downstream_pad=0, lens={}
):
"""
Read a file into a dictionary of bitsets. The defaults arguments
- 'f' should be a file like object (or any iterable containing strings)
- 'chrom_col', 'start_col', and 'end_col' must exist in each line.
- 'strand_col' is optional, any line without it will be assumed to be '+'
- if 'lens' is provided bitset sizes will be looked up from it, otherwise
chromosomes will be assumed to be the maximum size
"""
last_chrom = None
last_bitset = None
bitsets = {}
for line in f:
if line.startswith("#") or line.isspace():
continue
fields = line.split()
chrom = fields[chrom_col]
if chrom != last_chrom:
if chrom not in bitsets:
if chrom in lens:
size = lens[chrom]
else:
size = MAX
bitsets[chrom] = BinnedBitSet(size)
last_chrom = chrom
last_bitset = bitsets[chrom]
start, end = int(fields[start_col]), int(fields[end_col])
if upstream_pad:
start = max(0, start - upstream_pad)
if downstream_pad:
end = min(size, end + downstream_pad)
if start > end:
warn("Interval start after end!")
last_bitset.set_range(start, end - start)
return bitsets
def binned_bitsets_from_bed_file(
f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream_pad=0, downstream_pad=0, lens={}
):
"""
Read a file into a dictionary of bitsets. The defaults arguments
- 'f' should be a file like object (or any iterable containing strings)
- 'chrom_col', 'start_col', and 'end_col' must exist in each line.
- 'strand_col' is optional, any line without it will be assumed to be '+'
- if 'lens' is provided bitset sizes will be looked up from it, otherwise
chromosomes will be assumed to be the maximum size
"""
last_chrom = None
last_bitset = None
bitsets = {}
offset = 0
for line in f:
if line.startswith("#") or line.isspace():
continue
# Ignore browser lines completely
if line.startswith("browser"):
continue
# Need to check track lines due to the offset
if line.startswith("track"):
m = re.search(r"offset=(\d+)", line)
if m and m.group(1):
offset = int(m.group(1))
continue
fields = line.split()
chrom = fields[chrom_col]
if chrom != last_chrom:
if chrom not in bitsets:
if chrom in lens:
size = lens[chrom]
else:
size = MAX
bitsets[chrom] = BinnedBitSet(size)
last_chrom = chrom
last_bitset = bitsets[chrom]
start, end = int(fields[start_col]) + offset, int(fields[end_col]) + offset
if upstream_pad:
start = max(0, start - upstream_pad)
if downstream_pad:
end = min(size, end + downstream_pad)
if start > end:
warn("Interval start after end!")
last_bitset.set_range(start, end - start)
return bitsets
def binned_bitsets_proximity(f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream=0, downstream=0):
"""Read a file into a dictionary of bitsets"""
last_chrom = None
last_bitset = None
bitsets = {}
for line in f:
if line.startswith("#"):
continue
fields = line.split()
strand = "+"
if len(fields) >= strand_col + 1:
if fields[strand_col] == "-":
strand = "-"
chrom = fields[chrom_col]
if chrom != last_chrom:
if chrom not in bitsets:
bitsets[chrom] = BinnedBitSet(MAX)
last_chrom = chrom
last_bitset = bitsets[chrom]
start, end = int(fields[start_col]), int(fields[end_col])
if strand == "+":
if upstream:
start = max(0, start - upstream)
if downstream:
end = min(MAX, end + downstream)
if strand == "-":
if upstream:
end = min(MAX, end + upstream)
if downstream:
start = max(0, start - downstream)
if end - start > 0:
last_bitset.set_range(start, end - start)
return bitsets
def binned_bitsets_from_list(list=[]):
"""Read a list into a dictionary of bitsets"""
last_chrom = None
last_bitset = None
bitsets = {}
for l in list:
chrom = l[0]
if chrom != last_chrom:
if chrom not in bitsets:
bitsets[chrom] = BinnedBitSet(MAX)
last_chrom = chrom
last_bitset = bitsets[chrom]
start, end = int(l[1]), int(l[2])
last_bitset.set_range(start, end - start)
return bitsets
def binned_bitsets_by_chrom(f, chrom, chrom_col=0, start_col=1, end_col=2):
"""Read a file by chrom name into a bitset"""
bitset = BinnedBitSet(MAX)
for line in f:
if line.startswith("#"):
continue
fields = line.split()
if fields[chrom_col] == chrom:
start, end = int(fields[start_col]), int(fields[end_col])
bitset.set_range(start, end - start)
return bitset
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