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extract_promoter_regions.py
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extract_promoter_regions.py
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#!/usr/bin/env python3
import Mikado
import pyfaidx
import argparse
import sys
import collections
from Mikado.utilities.intervaltree import IntervalTree
import os
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import gzip
__doc__ = """Little script to extract promoter regions from genes."""
def main():
parser = argparse.ArgumentParser(__doc__)
parser.add_argument("-o", "--out", type=str, default="promoters")
parser.add_argument("-l", "--log", default=None)
parser.add_argument("-lv", "--log-level", default="WARN", choices=["DEBUG", "INFO", "WARN", "ERROR", "CRITICAL"],
dest="log_level")
parser.add_argument("-d", "--distances", nargs="+", type=int, default=[1000, 2000, 5000])
parser.add_argument("-nn", "--no-neighbours", dest="no_neighbours", action="store_true", default=False,
help="Ignore the presence of neighbours when extracting genes.")
parser.add_argument("-eu", "--exclude-utr", dest="exclude_utr", default=False, action="store_true")
parser.add_argument("-z", "--gzip", default=False, action="store_true",
help="Output will be compressed in GZip format.")
parser.add_argument("genome")
parser.add_argument("gff3")
parser.add_argument("gene_list")
args = parser.parse_args()
logger = Mikado.utilities.log_utils.create_logger_from_conf({"log_settings": {"log": args.log,
"log_level": args.log_level}},
"extractor",
mode="w")
max_distance = max(args.distances)
out_files = dict()
args.distances = sorted([_ for _ in args.distances if _ > 0])
if not args.distances:
exc = ValueError("I need at least one positive integer distance!")
logger.exception(exc)
sys.exit(1)
for distance in args.distances:
if args.gzip is True:
out_files[distance] = gzip.open("{}-{}bp.fasta.gz".format(os.path.splitext(args.out)[0],
distance), "wt")
else:
out_files[distance] = open("{}-{}bp.fasta".format(os.path.splitext(args.out)[0],
distance), "wt")
logger.info("Starting to load the genome")
genome = pyfaidx.Fasta(args.genome)
logger.info("Loaded the genome")
logger.info("Starting to load the GFF3 index")
with open(args.gff3) as gff3:
namespace = argparse.Namespace
namespace.reference = gff3
namespace.exclude_utr = args.exclude_utr
namespace.protein_coding = False
# Use Mikado compare functions to load the index from the GFF3
# "genes" is a dictionary of Gene objects, having as keys the gene names
# "positions" is a dictionary of the form: [chrom][(start, end)] = [GID1, GID2, ...]
genes, positions = Mikado.scales.compare.load_index(args, logger)
# Create a dictionary of interval trees, one per chromosome
indexer = collections.defaultdict(list).fromkeys(positions)
for chrom in indexer:
indexer[chrom] = IntervalTree.from_tuples(positions[chrom].keys())
logger.info("Loaded the index")
with open(args.gene_list) as gene_list:
gids = [_.rstrip() for _ in gene_list]
logger.info("Starting to extract sequences for {} genes".format(len(gids)))
for gid in gids:
if gid not in genes:
exc = IndexError("{} not found in the index!".format(gid))
logger.exception(exc)
continue
chrom, start, end, strand = (genes[gid].chrom,
genes[gid].start,
genes[gid].end,
genes[gid].strand)
if chrom not in genome:
exc = IndexError("Chromosome {} not found in the genome!".format(chrom))
logger.exception(exc)
continue
# If the gene is on the minus strand, the promoter is further down
if strand == "-":
key = (start, min(end + max_distance, len(genome[chrom])))
else:
# otherwise it is on the 5' side
key = (max(0, start - max_distance), end)
# Find all genes which are near
if args.no_neighbours is False:
neighbours = Mikado.scales.assigner.Assigner.find_neighbours(indexer.get(chrom, IntervalTree()),
key, distance=0)
# This is a list of the form [((start, end), distance), ...] where "(start, end)" is a key for the
# "positions" dictionary, above
# Find all the genes which are in the neighbourhood, remove the obvious case of the identity ..
def is_before(gid_coords, key, strand):
if strand == "-":
return (Mikado.utilities.overlap(gid_coords, key) >= 0) or gid_coords[1] < key[0]
else:
return (Mikado.utilities.overlap(gid_coords, key) >= 0) or gid_coords[0] > key[1]
neighbours = [_[0] for _ in neighbours if
is_before((start, end), _[0], strand) and gid not in positions[chrom][_[0]]]
else:
neighbours = []
if not neighbours:
# No neighbours found, we can grab everything
for distance in args.distances:
try:
if strand == "-":
chunk = (max(0, end), min(end + distance, len(genome[chrom])))
seq = genome[chrom][chunk[0]:chunk[1]].reverse.complement.seq
else:
chunk = (max(0, start - 1 - distance), start - 1)
seq = genome[chrom][chunk[0]:chunk[1]].seq
seq = SeqRecord(Seq(seq), id="{}-prom-{}".format(gid, distance),
description="{}{}:{}-{}".format(chrom, strand, chunk[0], chunk[1]))
print(seq.format("fasta"), file=out_files[distance], end='')
except ValueError as err:
logger.error("Error extracting the promoter for %s, distance %d. Error:\n%s",
gid, distance, err)
continue
else:
# We have some neighbours, we have to select the maximum distance we can go to
logger.warning("{} neighbours found for {}: {}".format(len(neighbours), gid, neighbours))
if any([Mikado.utilities.overlap((start, end), _) >= 0 for _ in neighbours]):
logger.warning("Overlapping genes found for {}. Skipping".format(gid))
continue
for distance in args.distances:
try:
if strand == "-":
max_point = min([_[0] for _ in neighbours])
if end + distance > max_point:
continue
chunk = (max(0, end), min(max_point, min(end + distance, len(genome[chrom]))))
seq = genome[chrom][chunk[0]:chunk[1]].reverse.complement.seq
description = "{}{}:{}-{}".format(chrom, strand, chunk[1], chunk[0])
else:
min_point = max([_[1] for _ in neighbours])
if start - distance < min_point:
continue
chunk = (max(0, start - 1 - distance), start - 1)
seq = genome[chrom][chunk[0]:chunk[1]].seq
description = "{}{}:{}-{}".format(chrom, strand, chunk[0], chunk[1])
seq = SeqRecord(Seq(seq), id="{}-prom-{}".format(gid, distance),
description=description)
print(seq.format("fasta"), file=out_files[distance], end='')
except ValueError as err:
logger.error("Error extracting the promoter for %s, distance %d. Error:\n%s",
gid, distance, err)
continue
logger.info("Finished")
return
main.__doc__ = __doc__
if __name__ == "__main__":
main()