From 9bb60bb18ae5ac70fe480095554796b7c18f1b6c Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 25 May 2018 15:52:40 +0000 Subject: Fixed issue causing anonymous collections to not work on my branch and staging, though still not sure why it's working on production without that change Added script to convert the dryad format genotype files to BIMBAM removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable --- wqflask/maintenance/quantile_normalize.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask/maintenance/quantile_normalize.py') diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index c11073fb..41a3aad8 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -59,7 +59,7 @@ def set_data(dataset_name): orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt" sample_list = [] - with open(orig_file, 'r') as orig_fh, open('quant_norm.csv', 'r') as quant_fh: + with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh: for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)): trait_dict = {} sample_list = [] @@ -118,7 +118,7 @@ if __name__ == '__main__': #out_filename = sys.argv[1][:-4] + '_quantnorm.txt' - #success, _ = bulk(es, set_data(sys.argv[1])) + success, _ = bulk(es, set_data(sys.argv[1])) response = es.search( index = "traits", doc_type = "trait", body = { -- cgit v1.2.3