Small changes to parse_gct, parse_gctx, and parse - Githubissues

cmap / cmapPy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

https://clue.io/cmapPy/index.html

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

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Small changes to parse_gct, parse_gctx, and parse #7

Closed levlitichev closed 7 years ago

levlitichev commented 7 years ago

Two main changes:

Making a copy of df in concat_gctoo to avoid warning
Added #VALUE! as another value to consider NaN in parse_gct.py (request from proteomics crew)

While I was in there, I made a few minor changes:

Previously, you could pass rid and cid as arguments to parse_gct, but then it would immediately break if you did; instead, I made it so that you can't even pass those args to parse_gct, but parse.py warns you that it will ignore those args (if parsing a GCT). I was thinking that errorring out is too severe.
Added a check in parse_gctx to make sure that the file exists. This makes the error message a little nicer.

@dllahr, @oena Let me know if these sound good.

oena commented 7 years ago

Looks good to me! Thanks @levlitichev.