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[datasets] deng et al. single cell experiment prints for ipython notebook

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Max Zwiessele 2014-10-06 11:00:57 +01:00
parent 919be3ceba
commit d93fac8c13
1 changed files with 4 additions and 3 deletions
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7
GPy/util/datasets.py
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@ -986,6 +986,7 @@ def singlecell_rna_seq_deng(dataset='singlecell_deng'):
# Extract the tar file # Extract the tar file
filename = os.path.join(dir_path, 'GSE45719_Raw.tar') filename = os.path.join(dir_path, 'GSE45719_Raw.tar')
with tarfile.open(filename, 'r') as files: with tarfile.open(filename, 'r') as files:
print "Extracting Archive {}...".format(files.name)
data = None data = None
gene_info = None gene_info = None
message = '' message = ''
@ -994,10 +995,9 @@ def singlecell_rna_seq_deng(dataset='singlecell_deng'):
for i, file_info in enumerate(members): for i, file_info in enumerate(members):
f = files.extractfile(file_info) f = files.extractfile(file_info)
inner = read_csv(f, sep='\t', header=0, compression='gzip', index_col=0) inner = read_csv(f, sep='\t', header=0, compression='gzip', index_col=0)
sys.stdout.write(' '*(len(message)+1) + '\r') print ' '*(len(message)+1) + '\r',
sys.stdout.flush()
message = "{: >7.2%}: Extracting: {}".format(float(i+1)/overall, file_info.name[:20]+"...txt.gz") message = "{: >7.2%}: Extracting: {}".format(float(i+1)/overall, file_info.name[:20]+"...txt.gz")
sys.stdout.write(message) print message,
if data is None: if data is None:
data = inner.RPKM.to_frame() data = inner.RPKM.to_frame()
data.columns = [file_info.name[:-18]] data.columns = [file_info.name[:-18]]
@ -1021,6 +1021,7 @@ def singlecell_rna_seq_deng(dataset='singlecell_deng'):
sys.stdout.write(' '*len(message) + '\r') sys.stdout.write(' '*len(message) + '\r')
sys.stdout.flush() sys.stdout.flush()
print
print "Read Archive {}".format(files.name) print "Read Archive {}".format(files.name)
return data_details_return({'Y': data, return data_details_return({'Y': data,