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| author | zsloan | 2018-05-25 15:52:40 +0000 |
|---|---|---|
| committer | zsloan | 2018-05-25 15:52:40 +0000 |
| commit | 9bb60bb18ae5ac70fe480095554796b7c18f1b6c (patch) | |
| tree | 58e1882cdb742e7d4a8e793a2545902fec803ece /wqflask/maintenance/quantile_normalize.py | |
| parent | 67e8f12e103f48329d8b3e38125c0e84b9dc089d (diff) | |
| download | genenetwork2-9bb60bb18ae5ac70fe480095554796b7c18f1b6c.tar.gz | |
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
Diffstat (limited to 'wqflask/maintenance/quantile_normalize.py')
| -rw-r--r-- | wqflask/maintenance/quantile_normalize.py | 4 |
1 files changed, 2 insertions, 2 deletions
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 = { |