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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,15 @@ | ||
| python2 ../utilities/SuSiEx_LD.py \ | ||
| --ref_file=EUR \ | ||
| --ld_file=EUR \ | ||
| --chr=1 \ | ||
| --bp=7314654,8314677 \ | ||
| --plink=../utilities/plink \ | ||
| --maf=0.005 | ||
| python2 ../utilities/SuSiEx_LD.py \ | ||
| --ref_file=AFR \ | ||
| --ld_file=AFR \ | ||
| --chr=1 \ | ||
| --bp=7314654,8314677 \ | ||
| --plink=../utilities/plink \ | ||
| --maf=0.005 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| #!/usr/bin/env python | ||
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| """ | ||
| SuSiEx_LD: LD calculation for SuSiEx | ||
| Usage: | ||
| python SuSiEx.py --ref_file=REF_FILE --ld_file=LD_MATRIX_FILE --chr=CHR --bp=BP --plink=PLINK --maf=MAF_THRESHOLD | ||
| """ | ||
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| import sys | ||
| import getopt | ||
| import subprocess | ||
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| def parse_param(): | ||
| long_opts_list = ['ref_file=', 'ld_file=', 'chr=', 'bp=', 'plink=', 'maf='] | ||
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| param_dict = {'ref_file': None, 'ld_file': None, 'chr': None, 'bp': None, 'plink': None, 'maf': 0.005} | ||
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| print('\n') | ||
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| if len(sys.argv) > 1: | ||
| try: | ||
| opts, args = getopt.getopt(sys.argv[1:], "h", long_opts_list) | ||
| except: | ||
| print('Option not recognized.') | ||
| print('Use --help for usage information.\n') | ||
| sys.exit(2) | ||
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| for opt, arg in opts: | ||
| if opt == "-h" or opt == "--help": | ||
| print(__doc__) | ||
| sys.exit(0) | ||
| elif opt == "--ref_file": param_dict['ref_file'] = arg | ||
| elif opt == "--ld_file": param_dict['ld_file'] = arg | ||
| elif opt == "--chr": param_dict['chr'] = int(arg) | ||
| elif opt == "--bp": param_dict['bp'] = map(int, arg.split(',')) | ||
| elif opt == "--plink": param_dict['plink'] = arg | ||
| elif opt == "--maf": param_dict['maf'] = float(arg) | ||
| else: | ||
| print(__doc__) | ||
| sys.exit(0) | ||
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| if param_dict['ref_file'] == None: | ||
| print('* Please provide the directory and filename prefix of the reference panel using --ref_file\n') | ||
| sys.exit(2) | ||
| elif param_dict['ld_file'] == None: | ||
| print('* Please provide the directory and filename prefix of the LD matrix to be computed using --ld_file\n') | ||
| sys.exit(2) | ||
| elif param_dict['chr'] == None: | ||
| print('* Please provide the chromosome code of the fine-mapping region using --chr\n') | ||
| sys.exit(2) | ||
| elif param_dict['bp'] == None or len(param_dict['bp']) != 2: | ||
| print('* Please provide the start and end base pair coordinate of the fine-mapping region using --bp\n') | ||
| sys.exit(2) | ||
| elif param_dict['plink'] == None: | ||
| print('* Please provide the directory and filename of PLINK using --plink\n') | ||
| sys.exit(2) | ||
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| for key in param_dict: | ||
| print('--%s=%s' % (key, param_dict[key])) | ||
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| print('\n') | ||
| return param_dict | ||
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| def main(): | ||
| param_dict = parse_param() | ||
| print('... calculate LD matrix ...') | ||
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| SNP = [] | ||
| with open(param_dict['ref_file']+'.bim') as ff: | ||
| for line in ff: | ||
| ll = (line.strip()).split() | ||
| if int(ll[0]) == param_dict['chr'] and int(ll[3]) >= param_dict['bp'][0] and int(ll[3]) <= param_dict['bp'][1]: | ||
| SNP.append(ll[1]) | ||
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| with open(param_dict['ld_file']+'.snp', 'w') as ff: | ||
| for snp in SNP: | ||
| ff.write('%s\n' % snp) | ||
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| cmd = '%s --bfile %s --keep-allele-order --chr %d --extract %s --maf %f --make-bed --out %s' \ | ||
| % (param_dict['plink'], param_dict['ref_file'], param_dict['chr'], param_dict['ld_file']+'.snp', param_dict['maf'], param_dict['ld_file']+'_ref') | ||
| subprocess.check_output(cmd, shell=True) | ||
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| cmd = '%s --bfile %s --keep-allele-order --r square bin4 --out %s' %(param_dict['plink'], param_dict['ld_file']+'_ref', param_dict['ld_file']) | ||
| subprocess.check_output(cmd, shell=True) | ||
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| cmd = '%s --bfile %s --keep-allele-order --freq --out %s' %(param_dict['plink'], param_dict['ld_file']+'_ref', param_dict['ld_file']+'_frq') | ||
| subprocess.check_output(cmd, shell=True) | ||
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| subprocess.check_output('rm '+param_dict['ld_file']+'.snp', shell=True) | ||
| subprocess.check_output('rm -rf '+param_dict['ld_file']+'.nosex', shell=True) | ||
| subprocess.check_output('rm -rf '+param_dict['ld_file']+'_*nosex', shell=True) | ||
| subprocess.check_output('rm '+param_dict['ld_file']+'_ref.bed', shell=True) | ||
| subprocess.check_output('rm '+param_dict['ld_file']+'_ref.fam', shell=True) | ||
| subprocess.check_output('rm '+param_dict['ld_file']+'_ref.log', shell=True) | ||
| subprocess.check_output('rm '+param_dict['ld_file']+'_frq.log', shell=True) | ||
| subprocess.check_output('rm '+param_dict['ld_file']+'.log', shell=True) | ||
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| print('... Done ...\n') | ||
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| if __name__ == '__main__': | ||
| main() | ||
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