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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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Problems parsing gctx due to meta_only #6

Closed joaoreis92 closed 7 years ago

joaoreis92 commented 7 years ago

Hi there. I'm being unable to parse a .gctx file. I think that's because of line 51 in parse.py which calls for parse_gctx.parse with an argument meta_only which is not defined. Thanks

dllahr commented 7 years ago

Can you send us the exact lines of code you were trying to use and the exact error message you received?

oena commented 7 years ago

Also, which version of cmapPy are you using? We're in the process of making some updates including changing the metadata syntax slightly; meta_only is an argument in versions 1.0.9 and prior but not later.

joaoreis92 commented 7 years ago

I was running the parse_gctx() function and the version has been cloned from github around the time I wrote here. I don't recall the error and don't have that version anymore but was something like "local variable 'meta_only' referenced before assignment"

The issue is now solved with the new commit, as the line containing the variable 'meta_only' was removed from the parse_gctx() function of parse_gctx.py file.

oena commented 7 years ago

Ok, thanks for the update @joaoreis92. Glad it's no longer a problem!