From 1041ba5a8f80b44eb845711077ac1704eff1282c Mon Sep 17 00:00:00 2001 From: Frank Vogt Date: Sat, 27 May 2023 17:46:31 +0200 Subject: [PATCH] v0.8.9 --- vcf2gwas/utils.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/vcf2gwas/utils.py b/vcf2gwas/utils.py index 587d91e..aa557c4 100644 --- a/vcf2gwas/utils.py +++ b/vcf2gwas/utils.py @@ -65,6 +65,8 @@ except ModuleNotFoundError: subprocess.run(["conda", "install", "-c", "conda-forge", "adjusttext==0.7*"]) from adjustText import adjust_text +import warnings +warnings.filterwarnings("ignore", message=".*The 'nopython' keyword.*") try: import umap except ModuleNotFoundError: @@ -1349,38 +1351,38 @@ def filter_snps(min_af, subset, subset2, chr): def make_bed(subset2, chrom, memory, threads, list1): """Description: - converts VCF file to PLINK BED files via plink""" + converts VCF file to PLINK BED files via plink2""" string = "_" list2 = [l for l in list1 if string in l] if list2 != []: if chrom <= 24: - make_bed = subprocess.run(['plink', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) + make_bed = subprocess.run(['plink2', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#\$r,\$a', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) make_bed.stdout make_bed.check_returncode() elif chrom <= 95: - make_bed = subprocess.run(['plink', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads), '--chr-set', str(chrom)], stdout=subprocess.PIPE, text=True) + make_bed = subprocess.run(['plink2', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#\$r,\$a', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads), '--chr-set', str(chrom)], stdout=subprocess.PIPE, text=True) make_bed.stdout make_bed.check_returncode() else: - make_bed = subprocess.run(['plink', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) + make_bed = subprocess.run(['plink2', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#\$r,\$a', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) make_bed.stdout make_bed.check_returncode() else: #make_bed = subprocess.run(['plink', '--dummy', '15000', '2000000', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--memory', str(memory),'--threads', str(threads), '--chr-set', str(chrom)], stdout=subprocess.PIPE, text=True) if chrom <= 24: - make_bed = subprocess.run(['plink', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) + make_bed = subprocess.run(['plink2', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#\$r,\$a', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) make_bed.stdout make_bed.check_returncode() elif chrom <= 95: - make_bed = subprocess.run(['plink', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--memory', str(memory),'--threads', str(threads), '--chr-set', str(chrom)], stdout=subprocess.PIPE, text=True) + make_bed = subprocess.run(['plink2', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#\$r,\$a', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads), '--chr-set', str(chrom)], stdout=subprocess.PIPE, text=True) make_bed.stdout make_bed.check_returncode() else: - make_bed = subprocess.run(['plink', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) + make_bed = subprocess.run(['plink2', '--vcf', f'{subset2}.vcf.gz', '--make-bed', '--out', subset2, '--mind', '1', '--set-missing-var-ids', '@:#\$r,\$a', '--allow-extra-chr', '--double-id', '--memory', str(memory),'--threads', str(threads)], stdout=subprocess.PIPE, text=True) make_bed.stdout make_bed.check_returncode() - + def remove_files(subset, File, subset2, snp_file): """Description: removes no longer needed files"""