| |
| import re |
| import click |
| import os |
| import glob |
| """ |
| script for running Beagle 5.4 |
| All kind of data for this script like human reference panel, genetic maps |
| and executable files for Beagle and Conform-gt can be found on the Beagle website |
| http://faculty.washington.edu/browning/beagle/beagle.html |
| """ |
|
|
|
|
| def bgzip_and_index(vcf, samples): |
| os.system(f'bcftools view {vcf} -Oz -o {vcf}.gz') |
| os.system(f'bcftools index {vcf}.gz') |
| if samples: |
| |
| os.system(f'bcftools view {samples} -Oz -o {samples}.gz') |
| os.system(f'bcftools index {samples}.gz') |
| print('bgzip_and_index: done') |
|
|
|
|
| def merge(vcf, samples): |
| os.system(f'bcftools merge {vcf}.gz {samples}.gz -o merged.vcf') |
| bgzip_and_index('merged.vcf', False) |
| print('merge: done') |
|
|
|
|
| def clean_and_gzip(vcf, samples): |
| if samples: |
| vcf = 'merged.vcf' |
| result_file = f'{vcf.split(".vcf")[0]}_clean.vcf' |
| os.system(f'bcftools view -e \'ALT =="." | REF=="."\' {vcf}.gz -Oz -o temp.vcf.gz') |
| os.system(f'bcftools norm -d none temp.vcf.gz >> {result_file}') |
| os.system(f'gzip {result_file}') |
| os.remove('temp.vcf.gz') |
| print('clean_and_gzip: done') |
| return f'{result_file}.gz' |
|
|
|
|
| def run_conform(conform, vcf_gz_file, ref_folder): |
| """output files: checked_{chr_type}.vcf.gz |
| docs: http://faculty.washington.edu/browning/conform-gt.html |
| reference: files was downloaded from from Beagle human reference link |
| https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/""" |
| for ref_file in glob.glob(f'{ref_folder}/**/chr*.vcf.gz', recursive=True): |
| print('conform ', ref_file) |
| if re.search("chr(\d+)", ref_file): |
| chr_type = (re.search("chr(\d+)", ref_file))[1] |
| elif re.search("chrX", ref_file): |
| chr_type = (re.search("chrX", ref_file))[0].split('chr')[1] |
| os.system(f'java -jar {conform} ref={ref_file} gt={vcf_gz_file} chrom={chr_type} ' |
| f'out=checked_{chr_type}') |
| print('run_conform: done') |
|
|
|
|
| def ensure_biallelic_ref(ref_dir): |
| for ref_file in glob.glob(f'{ref_dir}/chr*.v5a.vcf.gz'): |
| ref_biall_path = os.path.join(ref_dir, f'{ref_file.split("vcf")[0]}biallelic.vcf.gz') |
| print('ensure ', ref_file, ref_biall_path) |
| os.system(f'bcftools view -m2 -M2 -v snps -Oz -o {ref_biall_path} {ref_file}') |
| os.system(f'bcftools index {ref_biall_path}.gz') |
| os.remove(ref_file) |
|
|
|
|
| def run_beagle(beagle, gb, map_dir, ref_dir): |
| """output files: checked_{chr_type}.vcf.gz |
| docs: http://faculty.washington.edu/browning/conform-gt.html""" |
| for checked_file in glob.glob(f'{os.getcwd()}/checked_*.vcf.gz'): |
| if re.search("checked_(\d+)", checked_file): |
| chr_type = (re.search("checked_(\d+)", checked_file))[1] |
| elif re.search("checked_X", checked_file): |
| chr_type = (re.search("checked_X", checked_file))[0].split('checked_')[1] |
| for ref_file in glob.glob(f'{ref_dir}/chr{chr_type}.*biallelic.vcf.gz'): |
| for map_file in glob.glob(f'{map_dir}/plink.chr{chr_type}.*.map'): |
| os.system(f'java -Xmx{gb}g -jar {beagle} gt={checked_file} ref={ref_file}' |
| f' out=imputed_{chr_type} map={map_file}') |
|
|
|
|
| @click.command() |
| @click.option('--vcf', help='Path to the target vcf file') |
| @click.option('--samples', help='Path to VCF with other samples for conform checks, not required if target VCF' |
| 'contains data for at least 20 individuals', required=False) |
| @click.option('--conform', help='Path to conform .jar file') |
| @click.option('--beagle', help='Path to beagle .jar file') |
| @click.option('--ref', help='Path to folder with reference genome:' |
| ' .vcf.gz files are expected to start with "chr1."..."chr22.", "chrX."') |
| @click.option('--map', help='Path to folder with PLINK format genetic maps, files are expected to start with' |
| '"plink.chr1.", ..."plink.chr22.", "plink.chrX."') |
| @click.option('--gb', help='Number of gigabytes for running beagle', default=10, show_default=True) |
| def main(vcf, samples, conform, beagle, ref, map, gb): |
| bgzip_and_index(vcf, samples) |
| if samples: |
| merge(vcf, samples) |
| cleaned_file = clean_and_gzip(vcf, samples) |
| ensure_biallelic_ref(ref) |
| run_conform(conform, cleaned_file, ref) |
| run_beagle(beagle, gb, map, ref) |
|
|
|
|
| main() |
|
|
