/
calculate_divergence_bysnp.py
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calculate_divergence_bysnp.py
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import re
import gzip
import glob
import subprocess
import argparse
import random
from itertools import izip
def get_variants(vcf, sp, chr):
haps = {}
f = gzip.open(vcf, 'r')
nind = None
for l in f:
if not re.search('#', l):
d = re.split('\t', l.rstrip())
# check not indel
indel = False
alleles = [d[3]] + re.split(',', d[4])
for allele in alleles:
if len(allele) > 1:
indel = True
num_alleles = {}
for ix, allele in enumerate(alleles):
num_alleles[str(ix)] = allele
num_alleles['.'] = 'N'
if not indel:
genos = []
for geno in d[9:]:
geno = re.search('^([^:]+)', geno).group(1)
if re.search('/', geno):
geno = re.split('/', geno)
random.shuffle(geno)
genos += geno
else:
genos += re.split('\|', geno)
genos = [num_alleles[x] for x in genos]
if sp == 'LTFh':
if chr == 'chrZ':
genos = genos[0:15]
else:
genos = genos[0:20]
if sp == 'LTFa':
if chr == 'chrZ':
genos = genos[15:32]
else:
genos = genos[20:40]
haps[int(d[1])] = genos
nind = len(genos)
f.close()
return haps, nind
def get_sequence(ref_genome, genome1, genome2, chr, start, end):
seq_call = subprocess.Popen('samtools faidx %s %s:%s-%s' % (genome1, chr, start, end), shell=True, stdout=subprocess.PIPE)
seq1 = ''
for l in seq_call.stdout:
if not re.match('>', l):
seq1 += l.rstrip().upper()
seq1 = list(seq1)
seq_call = subprocess.Popen('samtools faidx %s %s:%s-%s' % (genome2, chr, start, end), shell=True, stdout=subprocess.PIPE)
seq2 = ''
for l in seq_call.stdout:
if not re.match('>', l):
seq2 += l.rstrip().upper()
seq2 = list(seq2)
seq_call = subprocess.Popen('samtools faidx %s %s:%s-%s' % (ref_genome, chr, start, end), shell=True, stdout=subprocess.PIPE)
ref_seq = ''
for l in seq_call.stdout:
if not re.match('>', l):
ref_seq += l.rstrip().upper()
ref_seq = list(ref_seq)
keep_sites = {}
for ix, (ref, bp1, bp2) in enumerate(izip(ref_seq, seq1, seq2)):
pos = ix + start
if bp1 in ['0', '1', '2', '3'] and bp2 in ['0', '1', '2', '3']:
keep_sites[pos] = ref
return keep_sites
def get_divergence(start, end, hap1, nind1, hap2, nind2, keep_sites):
sites = sorted(set(hap1.keys() + hap2.keys()))
sites = [x for x in sites if x in keep_sites]
pi = 0
pi_sum = 0
for site in sites:
num_diff = 0
if site in hap1:
geno1 = hap1[site]
else:
geno1 = keep_sites[site]
if site in hap2:
geno2 = hap2[site]
else:
geno2 = keep_sites[site]
for i in geno1:
for j in geno2:
if i != j and i != 'N' and j != 'N':
num_diff += 1
pi_sum += num_diff / float(len(geno1) * len(geno2))
if len(keep_sites) > 0:
pi = pi_sum / float(len(keep_sites))
return pi
def get_divergence_within(start, end, hap, nind, keep_sites):
sites = sorted(hap.keys())
sites = [x for x in sites if x in keep_sites]
pi = 0
pi_sum = 0
for site in sites:
num_diff = 0
geno = hap[site]
for ix, i in enumerate(geno):
for j in geno[ix:]:
if i != j and i != 'N' and j != 'N':
num_diff += 1
pi_sum += (2 * num_diff) / float(len(geno) * len(geno))
if len(keep_sites) > 0:
pi = pi_sum / float(len(keep_sites))
return pi
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--sp1", help="species1 for which to run analysis")
parser.add_argument("--sp2", help="species2 for which to run analysis")
parser.add_argument("--chr", help="chromosome for which to run anlaysis")
args = parser.parse_args()
sp1 = args.sp1
sp2 = args.sp2
chr = args.chr
window = 10000
chr_lengths = { 'chr10': 20806668, 'chr11': 21403021, 'chr12': 21576510, 'chr13': 16962381,
'chr14': 16419078, 'chr15': 14428146, 'chr16': 9909, 'chr17': 11648728,
'chr18': 11201131, 'chr19': 11587733, 'chr1A': 73657157, 'chr1B': 1083483,
'chr1': 118548696, 'chr20': 15652063, 'chr21': 5979137, 'chr22': 3370227,
'chr23': 6196912, 'chr24': 8021379, 'chr25': 1275379, 'chr26': 4907541,
'chr27': 4618897, 'chr28': 4963201, 'chr2': 156412533, 'chr3': 112617285,
'chr4A': 20704505, 'chr4': 69780378, 'chr5': 62374962, 'chr6': 36305782,
'chr7': 39844632, 'chr8': 27993427, 'chr9': 27241186, 'chrLG2': 109741,
'chrLG5': 16416, 'chrLGE22': 883365, 'chrZ': 72861351}
vcfs = { 'ZF': '/mnt/gluster/home/sonal.singhal1/ZF/after_vqsr/by_chr/unrel_vcf/gatk.ug.unrel_zf.%s.coverage.repeatmasked.filtered.nomendel.shared.noswitch.phased.vqsr2.vcf.gz' % chr,
'LTF': '/mnt/gluster/home/sonal.singhal1/LTF/after_vqsr/by_chr/gatk.ug.ltf.%s.coverage.repeatmasked.filtered.phased.vqsr2.vcf.gz' % chr,
'DBF': '/mnt/gluster/home/sonal.singhal1/DBF/after_vqsr/by_chr/gatk.ug.dbf.%s.filtered.coverage.vqsr.vcf.gz' % chr,
'LTFh': '/mnt/gluster/home/sonal.singhal1/LTF/after_vqsr/by_chr/gatk.ug.ltf.%s.coverage.repeatmasked.filtered.phased.vqsr2.vcf.gz' % chr,
'LTFa': '/mnt/gluster/home/sonal.singhal1/LTF/after_vqsr/by_chr/gatk.ug.ltf.%s.coverage.repeatmasked.filtered.phased.vqsr2.vcf.gz' % chr
}
if chr == 'chrZ':
vcfs = { 'ZF': '/mnt/gluster/home/sonal.singhal1/ZF/after_vqsr/by_chr/unrel_vcf/gatk.ug.unrel_zf.chrZ.coverage.repeatmasked.filtered.nomendel.shared.recodedsex.phased.vqsr2.vcf.gz',
'LTF': '/mnt/gluster/home/sonal.singhal1/LTF/after_vqsr/by_chr/gatk.ug.ltf.chrZ.coverage.repeatmasked.filtered.recodedsex.phased.vqsr2.vcf.gz',
'DBF': '/mnt/gluster/home/sonal.singhal1/DBF/after_vqsr/by_chr/gatk.ug.dbf.chrZ.filtered.coverage.vqsr.vcf.gz',
'LTFh': '/mnt/gluster/home/sonal.singhal1/LTF/after_vqsr/by_chr/gatk.ug.ltf.chrZ.coverage.repeatmasked.filtered.recodedsex.phased.vqsr2.vcf.gz',
'LTFa': '/mnt/gluster/home/sonal.singhal1/LTF/after_vqsr/by_chr/gatk.ug.ltf.chrZ.coverage.repeatmasked.filtered.recodedsex.phased.vqsr2.vcf.gz'
}
genomes = { 'ZF': '/mnt/gluster/home/sonal.singhal1/ZF/masked_genome/ZF.masked_genome.repeat_masked.switch_masked.fa',
'LTF': '/mnt/gluster/home/sonal.singhal1/LTF/masked_genome/LTF.masked_genome.repeat_masked.fa',
'LTFh': '/mnt/gluster/home/sonal.singhal1/LTF/masked_genome/LTF.masked_genome.repeat_masked.fa',
'LTFa': '/mnt/gluster/home/sonal.singhal1/LTF/masked_genome/LTF.masked_genome.repeat_masked.fa',
'DBF': '/mnt/gluster/home/sonal.singhal1/DBF/masked_genome/DBF.masked_genome.fa'
}
ref_genome = '/mnt/gluster/home/sonal.singhal1/reference/Zfinch.fa'
out_file = '/mnt/gluster/home/sonal.singhal1/ZF/analysis/pop_gen/%s.%s_%s.pairwise_snps_divergence.csv' % (chr, sp1, sp2)
(hap1, nind1) = get_variants(vcfs[sp1], sp1, chr)
(hap2, nind2) = get_variants(vcfs[sp2], sp2, chr)
o = open(out_file, 'w')
o.write('chr,start,end,num_sites,dxy,dx,dy,da\n')
for start in range(1, chr_lengths[chr] + 1, window):
end = start + window - 1
if end > chr_lengths[chr]:
end = chr_lengths[chr]
keep_sites = get_sequence(ref_genome, genomes[sp1], genomes[sp2], chr, start, end)
dxy = get_divergence(start, end, hap1, nind1, hap2, nind2, keep_sites)
dx = get_divergence_within(start, end, hap1, nind1, keep_sites)
dy = get_divergence_within(start, end, hap2, nind2, keep_sites)
da = dxy - (dx + dy) / 2.0
o.write('%s,%s,%s,%s,%s,%s,%s,%s\n' % (chr, start, end, len(keep_sites), dxy, dx, dy, da))
o.close()
if __name__ == "__main__":
main()