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| #!/usr/bin/env python2
'''
The script converts a collection of SNPs in VCF format into a PHYLIP, FASTA,
NEXUS, or binary NEXUS file for phylogenetic analysis. The code is optimized
to process VCF files with sizes >1GB. For small VCF files the algorithm slows
down as the number of taxa increases (but is still fast).
Any ploidy is allowed, but binary NEXUS is produced only for diploid VCFs.
'''
__author__ = "Edgardo M. Ortiz"
__credits__ = "Juan D. Palacio-Mejía"
__version__ = "2.0"
__email__ = "e.ortiz.v@gmail.com"
__date__ = "2019-01-15"
import sys
import os
import argparse
import gzip
def main():
parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("-i", "--input", action="store", dest="filename", required=True,
help="Name of the input VCF file, can be gzipped")
parser.add_argument("-m", "--min-samples-locus", action="store", dest="min_samples_locus", type=int, default=4,
help="Minimum of samples required to be present at a locus, default=4 since is the minimum for phylogenetics.")
parser.add_argument("-o", "--outgroup", action="store", dest="outgroup", default="",
help="Name of the outgroup in the matrix. Sequence will be written as first taxon in the alignment.")
parser.add_argument("-p", "--phylip-disable", action="store_true", dest="phylipdisable", default=False,
help="A PHYLIP matrix is written by default unless you enable this flag")
parser.add_argument("-f", "--fasta", action="store_true", dest="fasta", default=False,
help="Write a FASTA matrix, disabled by default")
parser.add_argument("-n", "--nexus", action="store_true", dest="nexus", default=False,
help="Write a NEXUS matrix, disabled by default")
parser.add_argument("-b", "--nexus-binary", action="store_true", dest="nexusbin", default=False,
help="Write a binary NEXUS matrix for analysis of biallelic SNPs in SNAPP, disabled by default")
args = parser.parse_args()
filename = args.filename
if filename.endswith(".gz"):
opener = gzip.open
else:
opener = open
min_samples_locus = args.min_samples_locus
outgroup = args.outgroup
phylipdisable = args.phylipdisable
fasta = args.fasta
nexus = args.nexus
nexusbin = args.nexusbin
amb = {"*":"-", "A":"A", "C":"C", "G":"G", "N":"N", "T":"T",
"*A":"a", "*C":"c", "*G":"g", "*N":"n", "*T":"t",
"AC":"M", "AG":"R", "AN":"a", "AT":"W", "CG":"S",
"CN":"c", "CT":"Y", "GN":"g", "GT":"K", "NT":"t",
"*AC":"m", "*AG":"r", "*AN":"a", "*AT":"w", "*CG":"s",
"*CN":"c", "*CT":"y", "*GN":"g", "*GT":"k", "*NT":"t",
"ACG":"V", "ACN":"m", "ACT":"H", "AGN":"r", "AGT":"D",
"ANT":"w", "CGN":"s", "CGT":"B", "CNT":"y", "GNT":"k",
"*ACG":"v", "*ACN":"m", "*ACT":"h", "*AGN":"r", "*AGT":"d",
"*ANT":"w", "*CGN":"s", "*CGT":"b", "*CNT":"y", "*GNT":"k",
"ACGN":"v", "ACGT":"N", "ACNT":"h", "AGNT":"d", "CGNT":"b",
"*ACGN":"v", "*ACGT":"N", "*ACNT":"h", "*AGNT":"d", "*CGNT":"b",
"*ACGNT":"N"}
gen_bin = {"./.":"?",
".|.":"?",
"0/0":"0",
"0|0":"0",
"0/1":"1",
"0|1":"1",
"1/0":"1",
"1|0":"1",
"1/1":"2",
"1|1":"2"}
ploidy = 0
gt_idx = []
missing = ""
with opener(filename) as vcf:
sample_names = []
len_longest_name = 0
for line in vcf:
if line.startswith("#CHROM"):
broken = line.strip("\n").split("\t")
if min_samples_locus > len(broken[9:]):
min_samples_locus = len(broken[9:])
for i in range(9, len(broken)):
name_sample = broken[i].replace("./","")
sample_names.append(name_sample)
len_longest_name = max(len_longest_name, len(name_sample))
elif not line.startswith("#") and line.strip("\n") != "":
while ploidy == 0 and missing == "":
broken = line.strip("\n").split("\t")
for j in range(9, len(broken)):
if ploidy == 0:
if broken[j].split(":")[0][0] != ".":
ploidy = (len(broken[j].split(":")[0]) // 2) + 1
gt_idx = [i for i in range(0, len(broken[j].split(":")[0]), 2)]
missing = "/".join(["." for i in range(len(gt_idx))])
break
vcf.close()
print("\nConverting file " + filename + ":\n")
print("Number of samples in VCF: " + str(len(sample_names)))
if filename.endswith(".gz"):
outfile = filename.replace(".vcf.gz",".min"+str(min_samples_locus))
else:
outfile = filename.replace(".vcf",".min"+str(min_samples_locus))
if fasta or nexus or not phylipdisable:
temporal = open(outfile+".tmp", "w")
if nexusbin:
if ploidy == 2:
temporalbin = open(outfile+".bin.tmp", "w")
else:
print("Binary NEXUS not available for "+str(ploidy)+"-ploid VCF.")
nexusbin = False
index_last_sample = len(sample_names)+9
with opener(filename) as vcf:
snp_num = 0
snp_accepted = 0
snp_shallow = 0
snp_multinuc = 0
snp_biallelic = 0
while 1:
vcf_chunk = vcf.readlines(50000)
if not vcf_chunk:
break
for line in vcf_chunk:
if not line.startswith("#") and line.strip("\n") != "":
broken = line.strip("\n").split("\t")
for g in range(9,len(broken)):
if broken[g].split(":")[0][0] == ".":
broken[g] = missing
snp_num += 1
if snp_num % 500000 == 0:
print(str(snp_num)+" genotypes processed.")
if (len(broken[9:]) - ''.join(broken[9:]).count(missing)) >= min_samples_locus:
if len(broken[3]) == 1 and (len(broken[4])-broken[4].count(",")) == (broken[4].count(",")+1):
snp_accepted += 1
if fasta or nexus or not phylipdisable:
nuc = {str(0):broken[3], ".":"N"}
for n in range(len(broken[4].split(","))):
nuc[str(n+1)] = broken[4].split(",")[n]
site_tmp = ''.join([amb[''.join(sorted(set([nuc[broken[i][j]] for j in gt_idx])))] for i in range(9, index_last_sample)])
temporal.write(site_tmp+"\n")
if nexusbin:
if len(broken[4]) == 1:
snp_biallelic += 1
binsite_tmp = ''.join([(gen_bin[broken[i][0:3]]) for i in range(9, index_last_sample)])
temporalbin.write(binsite_tmp+"\n")
else:
snp_multinuc += 1
snp_shallow += 1
else:
snp_shallow += 1
print("Total of genotypes processed: " + str(snp_num))
print("Genotypes excluded because they exceeded the amount of missing data allowed: " + str(snp_shallow))
print("Genotypes that passed missing data filter but were excluded for not being SNPs: " + str(snp_multinuc))
print("SNPs that passed the filters: " + str(snp_accepted))
if nexusbin:
print("Biallelic SNPs selected for binary NEXUS: " + str(snp_biallelic))
print("")
vcf.close()
if fasta or nexus or not phylipdisable:
temporal.close()
if nexusbin:
temporalbin.close()
if not phylipdisable:
output_phy = open(outfile+".phy", "w")
header_phy = str(len(sample_names))+" "+str(snp_accepted)+"\n"
output_phy.write(header_phy)
if fasta:
output_fas = open(outfile+".fasta", "w")
if nexus:
output_nex = open(outfile+".nexus", "w")
header_nex = "#NEXUS\n\nBEGIN DATA;\n\tDIMENSIONS NTAX=" + str(len(sample_names)) + " NCHAR=" + str(snp_accepted) + ";\n\tFORMAT DATATYPE=DNA" + " MISSING=N" + " GAP=- ;\nMATRIX\n"
output_nex.write(header_nex)
if nexusbin:
output_nexbin = open(outfile+".bin.nexus", "w")
header_nexbin = "#NEXUS\n\nBEGIN DATA;\n\tDIMENSIONS NTAX=" + str(len(sample_names)) + " NCHAR=" + str(snp_biallelic) + ";\n\tFORMAT DATATYPE=SNP" + " MISSING=?" + " GAP=- ;\nMATRIX\n"
output_nexbin.write(header_nexbin)
idx_outgroup = "NA"
if outgroup in sample_names:
idx_outgroup = sample_names.index(outgroup)
if fasta or nexus or not phylipdisable:
with open(outfile+".tmp") as tmp_seq:
seqout = ""
for line in tmp_seq:
seqout += line[idx_outgroup]
if fasta:
output_fas.write(">"+sample_names[idx_outgroup]+"\n"+seqout+"\n")
padding = (len_longest_name + 3 - len(sample_names[idx_outgroup])) * " "
if not phylipdisable:
output_phy.write(sample_names[idx_outgroup]+padding+seqout+"\n")
if nexus:
output_nex.write(sample_names[idx_outgroup]+padding+seqout+"\n")
print("Outgroup, "+outgroup+", added to the matrix(ces).")
if nexusbin:
with open(outfile+".bin.tmp") as bin_tmp_seq:
seqout = ""
for line in bin_tmp_seq:
seqout += line[idx_outgroup]
padding = (len_longest_name + 3 - len(sample_names[idx_outgroup])) * " "
output_nexbin.write(sample_names[idx_outgroup]+padding+seqout+"\n")
print("Outgroup, "+outgroup+", added to the binary matrix.")
for s in range(0, len(sample_names)):
if s != idx_outgroup:
if fasta or nexus or not phylipdisable:
with open(outfile+".tmp") as tmp_seq:
seqout = ""
for line in tmp_seq:
seqout += line[s]
if fasta:
output_fas.write(">"+sample_names[s]+"\n"+seqout+"\n")
padding = (len_longest_name + 3 - len(sample_names[s])) * " "
if not phylipdisable:
output_phy.write(sample_names[s]+padding+seqout+"\n")
if nexus:
output_nex.write(sample_names[s]+padding+seqout+"\n")
print("Sample "+str(s+1)+" of "+str(len(sample_names))+", "+sample_names[s]+", added to the nucleotide matrix(ces).")
if nexusbin:
with open(outfile+".bin.tmp") as bin_tmp_seq:
seqout = ""
for line in bin_tmp_seq:
seqout += line[s]
padding = (len_longest_name + 3 - len(sample_names[s])) * " "
output_nexbin.write(sample_names[s]+padding+seqout+"\n")
print("Sample "+str(s+1)+" of "+str(len(sample_names))+", "+sample_names[s]+", added to the binary matrix.")
if not phylipdisable:
output_phy.close()
if fasta:
output_fas.close()
if nexus:
output_nex.write(";\nEND;\n")
output_nex.close()
if nexusbin:
output_nexbin.write(";\nEND;\n")
output_nexbin.close()
if fasta or nexus or not phylipdisable:
os.remove(outfile+".tmp")
if nexusbin:
os.remove(outfile+".bin.tmp")
print( "\nDone!\n")
if __name__ == "__main__":
main()
|