62 lines
1.8 KiB
Python
62 lines
1.8 KiB
Python
"""Find max depth window in a `mosdepth` regions BED file and write as locus string."""
|
|
|
|
from pathlib import Path
|
|
import sys
|
|
|
|
import pandas as pd
|
|
|
|
from .util import get_named_logger, wf_parser # noqa: ABS101
|
|
|
|
|
|
def main(args):
|
|
"""Run the entry point."""
|
|
logger = get_named_logger("getMaxDepth")
|
|
|
|
# read the regions BED file
|
|
df = pd.read_csv(
|
|
args.depths_bed, sep="\t", header=None, names=["ref", "start", "end", "depth"]
|
|
)
|
|
|
|
# get the window with the largest depth
|
|
ref, start, end, depth = df.loc[df["depth"].idxmax()]
|
|
|
|
# get the length of the reference of that window
|
|
ref_length = df.query("ref == @ref")["end"].iloc[-1]
|
|
|
|
# show the whole reference in case it's shorter than the desired locus size
|
|
if ref_length < args.locus_size:
|
|
start = 1
|
|
end = ref_length
|
|
else:
|
|
# otherwise, show a region of the desired size around the window
|
|
half_size = args.locus_size // 2
|
|
mid = (start + end) // 2
|
|
start = mid - half_size
|
|
end = mid + half_size
|
|
# check if the region starts below `1` or ends beyond the end of the reference
|
|
if start < 1:
|
|
start = 1
|
|
end = args.locus_size
|
|
if end > ref_length:
|
|
start = ref_length - args.locus_size
|
|
end = ref_length
|
|
|
|
# write depth and locus string
|
|
sys.stdout.write(f"{depth}\t{ref}:{start}-{end}")
|
|
|
|
logger.info("Wrote locus with maximum depth to STDOUT.")
|
|
|
|
|
|
def argparser():
|
|
"""Argument parser for entrypoint."""
|
|
parser = wf_parser("get_max_depth_locus")
|
|
parser.add_argument(
|
|
"depths_bed",
|
|
type=Path,
|
|
help="path to mosdepth regions depth file (can be compressed)",
|
|
)
|
|
parser.add_argument(
|
|
"locus_size", type=int, help="size of the locus in basepairs (e.g. '2000')"
|
|
)
|
|
return parser
|