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added hapmap3 as dataset

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Max Zwiessele 2014-02-05 09:07:18 +00:00
parent 65977825c0
commit 04a3102546
1 changed files with 3 additions and 2 deletions
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5
GPy/util/datasets.py
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@ -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)