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[datasets] rnaseq changed up

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This commit is contained in:
Max Zwiessele 2016-07-19 14:31:37 +01:00
parent e9bad5c18f
commit 30b34591bb
2 changed files with 14 additions and 4 deletions
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12
GPy/util/datasets.py
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@ -98,7 +98,7 @@ def data_available(dataset_name=None):
try:
from itertools import zip_longest
except ImportError:
from itertools import zip_longest as zip_longest
from itertools import izip_longest as zip_longest
dr = data_resources[dataset_name]
zip_urls = (dr['files'], )
if 'save_names' in dr: zip_urls += (dr['save_names'], )
@ -1033,14 +1033,18 @@ def singlecell_rna_seq_deng(dataset='singlecell_deng'):
data = inner.RPKM.to_frame()
data.columns = [file_info.name[:-18]]
gene_info = inner.Refseq_IDs.to_frame()
gene_info.columns = [file_info.name[:-18]]
gene_info.columns = ['NCBI Reference Sequence']
else:
data[file_info.name[:-18]] = inner.RPKM
gene_info[file_info.name[:-18]] = inner.Refseq_IDs
#gene_info[file_info.name[:-18]] = inner.Refseq_IDs
# Strip GSM number off data index
rep = re.compile('GSM\d+_')
data.columns = data.columns.to_series().apply(lambda row: row[rep.match(row).end():])
from pandas import MultiIndex
columns = MultiIndex.from_tuples([row.split('_', 1) for row in data.columns])
columns.names = ['GEO Accession', 'index']
data.columns = columns
data = data.T
# make sure the same index gets used