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from __future__ import print_function
from argparse import ArgumentParser
import os
import gzip
import pybedtools
def _open_file(in_file):
"""From bcbio code"""
_, ext = os.path.splitext(in_file)
if ext == ".gz":
return gzip.open(in_file, 'rb')
if ext in [".fastq", ".fq"]:
return open(in_file, 'r')
# default to just opening it
return open(in_file, "r")
def _lift_positions(line):
mi_s, mi_e = line[11], line[12]
snp_p = [e for e, f in enumerate(line) if f.startswith("rs")][0] - 1
if line[14] == "-":
rel_p = int(mi_e) - int(line[snp_p]) + 1
else:
rel_p = int(line[snp_p]) - int(mi_s) + 1
return rel_p
def _complement(nt, strand):
pairs = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
return nt if strand == "+" else pairs[nt]
def _get_mirna_name(attrs):
items = attrs.split(";")
return [i.split("=")[1] for i in items if i.startswith("Name")][0]
def _create_header(mirna, snp, out):
names = set()
h = []
last_h = ""
with _open_file(snp) as in_handle:
for line in in_handle:
if line.startswith("##") and not line.startswith("##contig"):
h.append(line.strip())
elif line.startswith("#CHROM"):
last_h = line.strip()
else:
break
with open(mirna) as in_handle:
for line in in_handle:
if not line.startswith("#"):
cols = line.strip().split("\t")
if cols[2] == "miRNA":
names.add(_get_mirna_name(cols[8]))
for name in names:
h.append("##contig=<ID=%s>" % name)
h.append(last_h)
return "\n".join(h)
def select_snps(mirna, snp, out):
"""
Use bedtools to intersect coordinates
"""
with open(out, 'w') as out_handle:
print(_create_header(mirna, snp, out), file=out_handle, end="")
snp_in_mirna = pybedtools.BedTool(snp).intersect(pybedtools.BedTool(mirna), wo=True)
for single in snp_in_mirna:
if single[10] == "miRNA" and len(single[3]) + len(single[4]) == 2:
line = []
rel_p = _lift_positions(single)
line.append(_get_mirna_name(single[16]))
line.append(str(rel_p))
line.append(single[2])
line.append(_complement(single[3], single[14]))
line.append(_complement(single[4], single[14]))
line.append(single[5])
line.append(single[6])
line.append(single[7])
print("\t".join(line), file=out_handle, end="")
return out
if __name__ == "__main__":
parser = ArgumentParser(description="task related to allele methylation specific")
parser.add_argument("--gtf", help="gtf file with miRNA annotation", required=1)
parser.add_argument("--vcf", help="vcf file with SNP variants", required=1)
parser.add_argument("--out", help="out put file.", required=1)
args = parser.parse_args()
mirna_snp = select_snps(args.gtf, args.vcf, args.out)
print("%s mapped to %s: %s" % (args.vcf, args.gtf, mirna_snp))
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