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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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In parse_GDS_columns(), unknown subset_types discarded #23

Closed n1mus closed 7 years ago

n1mus commented 7 years ago

I have varying outcomes with which subset_types I encounter per parse. Although I have not encountered the ones encoded set(['individual', 'disease_state']), I have had to make use of set(['dose', 'agent', 'time', 'gender']). So, in parse_GDS_columns, I modified the code to start out with an empty subset_ids and collected everything on the fly.

This turned out nicely as each subset_type was accounted for in each sample in the end, so in GDS.columns no rows were dropped during GDS.__init__().

guma44 commented 7 years ago

Hey, thanks for report. Can you give me an example or maybe make a pull request that we can discuss it further?