From 04a31025466a0dc99f675406df5ee5732310f24c Mon Sep 17 00:00:00 2001 From: Max Zwiessele Date: Wed, 5 Feb 2014 09:07:18 +0000 Subject: [PATCH] added hapmap3 as dataset --- GPy/util/datasets.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/GPy/util/datasets.py b/GPy/util/datasets.py index 30c09eaa..a878c1d8 100644 --- a/GPy/util/datasets.py +++ b/GPy/util/datasets.py @@ -467,7 +467,8 @@ def hapmap3(data_set='hapmap3'): '.info.pickle', '.nan.pickle']] if not reduce(lambda a,b: a and b, map(os.path.exists, preprocessed_data_paths)): - if not overide_manual_authorize and prompt_user("Preprocessing requires 17GB of memory and can take alot of time, continue? [Y/n]\n"): + if not overide_manual_authorize and prompt_user("Preprocessing requires 17GB " + "of memory and can take a long time, continue? [Y/n]\n"): print "Preprocessing required for further usage." return status = "Preprocessing data, please be patient..." @@ -513,7 +514,7 @@ def hapmap3(data_set='hapmap3'): status=write_status('encoding snps...', 70, status) # Encode the information for each gene in {-1,0,1}: status=write_status('encoding snps...', 73, status) - snps = (snpstr==ref[:,:,None]) + snps = (snpstr==ref[None,:,:]) status=write_status('encoding snps...', 76, status) snps = (snps*np.array([1,-1])[None,None,:]) status=write_status('encoding snps...', 78, status)