Some samples don't have table data!

guma44 / GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

BSD 3-Clause "New" or "Revised" License

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Some samples don't have table data! #36

Open halioui opened 6 years ago

halioui commented 6 years ago

I got the following error while parsing GSM2795971 SOFT file:

File "pandas/_libs/parsers.pyx", line 565, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file

guma44 commented 6 years ago

Hi, The file just do not have any tabular data. I will make a bug-fix to return an empty one.

guma44 commented 6 years ago

So this was an issue with python 3 only. I check now if there is anything in the file.

kmuench commented 4 years ago

Hello - I am encountering this issue also in Python 3 (all tables imported are empty). Are there any updates on this issue?

guma44 commented 4 years ago

Hi @kmuench, thanks for reporting. Could you give an example? I thought it was solved last time.

kmuench commented 4 years ago

Sure thing, thanks for checking it out. Here is the code I'm running:

import GEOparse
# get sample info
gse = GEOparse.get_GEO(geo="GSE97168", destdir="./")
metadata = gse.phenotype_data # pandas data frame
samples = metadata.index.astype(str) 
s = samples[1]
gse.gsms[s].table.size

It does seem to identify the samples and the metadata - it's just the data stored that seems to be an issue.

CholoTook commented 3 years ago

What data are you expecting to see here? I don't see any here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2553018