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vcf_parser.py
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vcf_parser.py
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#!/usr/bin/python
# Copyright 2023 Simon Joly under the terms of the GNU General Public
# License as published by the Free Software Foundation, either version
# 3 of the License, or (at your option) any later version.
# Adapted from script described below to handle loci along chromosomes.
# It also fixes a bug in the --center-snp option.
# Copyright 2015 Diogo N. Silva <o.diogosilva@gmail.com>
# compare_pairs.py is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# Loci_counter is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with Loci_counter. If not, see <http://www.gnu.org/licenses/>.
# vcf_parser.py is that performs filtering and transformations steps on
# a VCF file that are not possible with vcftools
# Usage: python3 vcf_parser.py -h (will show all available options)
import argparse
import random
from collections import Counter
PARSER = argparse.ArgumentParser(description="Filtering of VCF files")
PARSER.add_argument("-vcf", dest="vcf_infile", help="Provide VCF "
" file(s).", required=True)
PARSER.add_argument("--remove-inv", dest="remove_inv", const=True,
action="store_const", help="Filters invariable SNP sites"
" from the VCF file (These sites may occurr when "
"individuals are removed from a VCF file).")
PARSER.add_argument("--remove-singletons", dest="remove_singletons", const=True,
action="store_const", help="Filters singletons SNP sites"
" from the VCF file.")
PARSER.add_argument("--one-snp", dest="one_snp", const=True,
action="store_const", help="Filters the VCF file so that"
" only one SNP per locus is retained - The first one")
PARSER.add_argument("--random-snp", dest="rnd_snp", const=True,
action="store_const", help="Filters the VCF file so that"
" only one random SNP per locus is retained.")
PARSER.add_argument("--center-snp", dest="center_snp", const=True,
action="store_const", help="Filters the VCF file so that"
" only the SNP closest to the locus center is retained.")
ARG = PARSER.parse_args()
def remove_sites(vcf_file, mode="inv", suffix="_NoInv.vcf"):
"""
Removes invariable sites from a VCF file. This assumes that the genotype
columns start at the 10th column until the last column
:param vcf_file: string, path to vcf file
:param mode: string, specifies the removal operation. May be one of the
following:
.:"inv": Removes invariable sites
.:"singletons": Removes singleton sites
:param suffix: string, the suffix of the output file.
"""
vcf_output = vcf_file.split(".")[0] + suffix
with open(vcf_file) as vcf_handle, open(vcf_output, "w") as vcf_out:
for line in vcf_handle:
if line.startswith("#"):
vcf_out.write(line)
elif line.strip() != "":
# Get genotypes. Remove genotypes with no data.
genotypes = [x.split(":")[0] for x in line.split()[9:] if x.split(":")[0] != "./."]
if mode == "inv":
# If number of unique genotypes higher than 1, save SNP
if len(set(genotypes)) > 1:
vcf_out.write(line)
elif mode == "singletons":
gens = Counter(genotypes)
# Remove most common genotype
del gens[gens.most_common()[0][0]]
# Check if remaining genotype count is higher than 1
if sum(gens.values()) > 1:
vcf_out.write(line)
def filter_one_snp(vcf_file):
"""
Filters a VCF file so that only one SNP per locus (the first) is retained
"""
vcf_output = vcf_file.split(".")[0] + "OneSNP.vcf"
locus_list = []
with open(vcf_file) as vcf_handle, open(vcf_output, "w") as vcf_out:
for line in vcf_handle:
if line.startswith("#"):
vcf_out.write(line)
elif line.strip() != "":
# Get chromosome
chrom = line.split()[0]
# Get locus
locus_position = line.split()[2]
locus = locus_position.split("_")[0]
# Append chromosome to locus name
locus = chrom + "_" + locus
if locus not in locus_list:
vcf_out.write(line)
locus_list.append(locus)
def filter_random_snp(vcf_file):
"""
Filters a VCF file so that only one random SNP per locus is retained.
"""
vcf_output = vcf_file.split(".")[0] + "RandSNP.vcf"
current_locus = ""
loci_snps = []
with open(vcf_file) as vcf_handle, open(vcf_output, "w") as vcf_out:
for line in vcf_handle:
if line.startswith("#"):
vcf_out.write(line)
elif line.strip() != "":
# Get chromosome
chrom = line.split()[0]
# Get locus
locus_position = line.split()[2]
locus = locus_position.split("_")[0]
# Append chromosome to locus name
locus = chrom + "_" + locus
if locus != current_locus and loci_snps != []:
choosen = random.choice(loci_snps)
vcf_out.write(choosen)
loci_snps = [line]
current_locus = locus
elif locus != current_locus and loci_snps == []:
loci_snps = [line]
current_locus = locus
else:
loci_snps += [line]
vcf_out.write(random.choice(loci_snps))
def filter_center_snp(vcf_file):
"""
Filters a VCF file so that only one SNP per locus (the first) is retained
"""
vcf_output = vcf_file.split(".")[0] + "CenterSNP.vcf"
current_locus = ""
line_list = []
pos_list = []
with open(vcf_file) as vcf_handle, open(vcf_output, "w") as vcf_out:
for line in vcf_handle:
if line.startswith("#"):
vcf_out.write(line)
elif line.strip() != "":
# Get chromosome
chrom = line.split()[0]
# Get locus
locus_position = line.split()[2]
locus = locus_position.split("_")[0]
# Append chromosome to locus name
locus = chrom + "_" + locus
# Get SNP position
pos = int(line.split()[1])
if locus != current_locus and current_locus != "":
mean_pos = sum(pos_list) / len(pos_list)
closest = min(pos_list, key=lambda x: abs(x - mean_pos))
vcf_out.write(line_list[pos_list.index(closest)])
pos_list = [pos]
line_list = [line]
current_locus = locus
elif locus != current_locus:
pos_list = [pos]
line_list = [line]
current_locus = locus
else:
pos_list += [pos]
line_list += [line]
mean_pos = sum(pos_list) / len(pos_list)
closest = min(pos_list, key=lambda x: abs(x - mean_pos))
vcf_out.write(line_list[pos_list.index(closest)])
def main():
"""
Main function that controls what to do.
"""
# Args
vcf_file = ARG.vcf_infile
if ARG.remove_inv:
remove_sites(vcf_file)
if ARG.remove_singletons:
remove_sites(vcf_file, mode="singletons", suffix="_NoSing.vcf")
if ARG.one_snp:
filter_one_snp(vcf_file)
if ARG.rnd_snp:
filter_random_snp(vcf_file)
if ARG.center_snp:
filter_center_snp(vcf_file)
main()