ccmpred should use "-r" instead of -b

luoyunan / ECNet

An evolutionary context-integrated deep learning framework for protein engineering

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

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ccmpred should use "-r" instead of -b #4

Closed Ced3-han closed 2 years ago

Ced3-han commented 2 years ago

ccmpred doesn't have "-b" option, instead we should use "-r" for raw output

ccmpred example.psc example.mat -r example.braw -d 0

jrhorne commented 2 years ago

Yes, this should be updated in the docs. Thank you! 👍

jrhorne commented 2 years ago

Okay, this issue wasn't as simple as I first thought. Updating here for anyone else running into this issue.

You do need CCMpred to output with the -b flag, as that is what msgpack needs for ECNet.
The reason this causes issues is that you need to have libmsgpack-dev available when compiling CCMpred for that option to be available.

To fix this issue on Ubuntu:

sudo apt update then sudo apt install libmsgpack-dev
Then recompile and install CCMpred according to here https://github.com/soedinglab/CCMpred
You should have the -b flag available now when running ccmpred -h

Better docs in both packages might help alleviate these issues for getting local features

luoyunan commented 2 years ago

Thanks @Ced3-han and @jrhorne!

The -b flag is only available in the latest branch but not in the release of CCMPred. Actually this has been mentioned in the document (step 1 in the feature generation section).

I will update the doc to say this more explicitly. Thanks for the suggestion!

jrhorne commented 2 years ago

Thanks! I know this is on CCMpred, but it took some digging here to realize I needed msgpack available first, otherwise the option never shows.

luoyunan commented 2 years ago

Thanks so much for the feedback!

luoyunan commented 2 years ago

Doc was revised in https://github.com/luoyunan/ECNet/commit/436eb6cec6d28697a04ce9d30433961731659139