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guma44 / GEOparse

Python library to access Gene Expression Omnibus Database (GEO)
BSD 3-Clause "New" or "Revised" License
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no columns at GSE #20

Closed antonkulaga closed 7 years ago

antonkulaga commented 7 years ago

When I try 

gse = GEOparse.get_GEO(geo="GSE69263", destdir="./")
gse.columns

I get:

gse.columns
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'GSE' object has no attribute 'columns'

while in the docs it is mentioned that columns is a standard GSE property

guma44 commented 7 years ago

Hi,

GSE object has no columns attribute. It is a container for GSMs. You can access each GSM in GSE with:

gse.gsms

Anyway the data is empty:

>>> print gse.gsms.values()[0].columns
Empty DataFrame
Columns: [description]
Index: []
antonkulaga commented 7 years ago

GSE object has no columns attribute.

In such case, you should fix the docs https://geoparse.readthedocs.io/en/latest/usage.html#gse-series as columns is mentioned there as standard GSE property.

guma44 commented 7 years ago

Hey, Indeed. The description is OK but the name is wrong. Thanks!