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[datasets] deng et all, labels revisited

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This commit is contained in:
Max Zwiessele 2014-10-10 11:07:07 +01:00
parent c128c6f948
commit 9b3498a912
1 changed files with 17 additions and 3 deletions
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20
GPy/util/datasets.py
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@ -964,7 +964,7 @@ def singlecell_rna_seq_deng(dataset='singlecell_deng'):
if not data_available(dataset):
download_data(dataset)
from pandas import read_csv
from pandas import read_csv, isnull
dir_path = os.path.join(data_path, dataset)
# read the info .soft
@ -983,6 +983,21 @@ def singlecell_rna_seq_deng(dataset='singlecell_deng'):
c[1:4] = ['strain', 'cross', 'developmental_stage']
sample_info.columns = c
# get the labels right:
rep = re.compile('\(.*\)')
def filter_dev_stage(row):
if isnull(row):
row = "2-cell stage embryo"
if row.startswith("developmental stage: "):
row = row[len("developmental stage: "):]
if row == 'adult':
row += " liver"
row = row.replace(' stage ', ' ')
row = rep.sub(' ', row)
row = row.strip(' ')
return row
labels = sample_info.developmental_stage.apply(filter_dev_stage)
# Extract the tar file
filename = os.path.join(dir_path, 'GSE45719_Raw.tar')
with tarfile.open(filename, 'r') as files:
@ -1016,8 +1031,7 @@ def singlecell_rna_seq_deng(dataset='singlecell_deng'):
sample_info.index = data.index
# get the labels from the description
rep = re.compile('fibroblast|\d+-cell|embryo|liver|blastocyst|blastomere|zygote', re.IGNORECASE)
labels = sample_info.developmental_stage.apply(lambda row: " ".join(rep.findall(row)))
#rep = re.compile('fibroblast|\d+-cell|embryo|liver|early blastocyst|mid blastocyst|late blastocyst|blastomere|zygote', re.IGNORECASE)
sys.stdout.write(' '*len(message) + '\r')
sys.stdout.flush()