From df03af3c7e43ac41c54f676a4e80213259ac6867 Mon Sep 17 00:00:00 2001 From: Francois Aguet Date: Sun, 19 Jun 2016 22:40:24 -0400 Subject: [PATCH] Added 'exclude-samples' option --- python/run_FastQTL_threaded.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/python/run_FastQTL_threaded.py b/python/run_FastQTL_threaded.py index bb5dbfa..ed4e437 100755 --- a/python/run_FastQTL_threaded.py +++ b/python/run_FastQTL_threaded.py @@ -28,6 +28,8 @@ def get_cmd(args, chunk): cmd += ' --permute '+' '.join([str(p) for p in args.permute]) if args.seed: cmd += ' --seed '+args.seed + if args.exclude_samples: + cmd += ' --exclude-samples '+args.exclude_samples cmd += ' --chunk '+str(chunk)+' '+args.chunks\ + ' --out '+args.prefix+'_chunk{0:03d}.txt.gz'.format(chunk)\ + ' --log '+args.prefix+'_chunk{0:03d}.log'.format(chunk) @@ -56,6 +58,7 @@ def perm_worker(inputs): parser.add_argument('--ma_sample_threshold', default='0', help='Include only genotypes with >=ma_sample_threshold samples carrying the minor allele (default 0)') parser.add_argument('--fdr', default=0.05, type=np.double) parser.add_argument('--seed', default=None, help='Random number generator seed') +parser.add_argument('--exclude_samples', default=None, help='') parser.add_argument('-t', '--threads', default='8', help='Number of threads') parser.add_argument('-o', '--output_dir', default='.', help='Output directory') args = parser.parse_args()