vcf2sweepfinder.py

import gzip
import csv
import argparse
import sys

parser = argparse.ArgumentParser(description="script to convert an all sites vcf to sweepfinder format. FASTA description will be the sample name in the VCF header.Only does one chromosome/region at a time.")
parser.add_argument("-v", "--vcf", action="store", required=True, help="Input VCF file. Should be a multisample vcf, though it should theoretically work with a single sample.")
parser.add_argument("-o", "--out", action="store", required=True, help="Output filename")
parser.add_argument("-c", "--chromosome", action="store", required=True, help="Chromosome to output. Should be something in the first column of the vcf.")
parser.add_argument("-g", "--gzip", action="store_true", required=False, help="Set if the VCF is gzipped.")

args = parser.parse_args()

vcf_in = args.vcf
out_name = args.out
out_chr = args.chromosome

sample_names = []
sample_seqs = []

if args.gzip:
    opener = gzip.open
else:
    opener = open

sweep_out = open(out_name, 'w')
sweep_out.write("position\tx\tn\tfolded\n") # write header
folded = "1"

with opener(vcf_in, 'r') as tsvin:
    tsvin = csv.reader(tsvin, delimiter='\t')

    for row in tsvin:
        if any('##' in strings for strings in row):
            continue
        if any('#CHROM' in strings for strings in row):
            sample_names = row[9:]
            for sample in sample_names:
                sample_seqs.append([""])
            continue

        chrom,pos,id,ref,alt,qual,filter,info,format=row[0:9]
        haplotypes = row[9:]

        location = pos

        if chrom == out_chr:
            alt_list = alt.split(",")
            x = 0
            n = 0
            for index,haplotype in enumerate(haplotypes):
                if haplotype.split(":")[0] != '.':
                    n = n + 1 # count up the non missing calls
                if haplotype.split(":")[0] != "0" and haplotype.split(":")[0] != ".":
                    x = x + 1 # count derived alleles = not reference and not missing
                
            if x != 0 and x != n:    
                sweep_out.write(location+"\t"+str(x)+"\t"+str(n)+"\t"+folded+"\n")
        else:
            continue

Hi, I am trying to parse the arguments to convert my vcf to sweeD format using vcf2sweepfinder.py, but I am not sure if the chromosome information I have (i.e., scaffold IDs such as contig00001) is in the proper format. The script does not give me any error message, so I do not know how to go about fixing. It just gives me the heading of the output file. Could you give me an example of how to run the script? Thank you in advance.

Hi, I am trying to convert my vcf to sweepinputfile using vcf2sweepfinder.py. My object is multiploidy, and is multi-sample in the vcf. But when I ran the scripts to generate the file, it turned out nothing in the output, and there is only the header in the output. Couly you give an example about how to run your script? Thank you.