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SorenKarst / longread_umi

GNU General Public License v3.0
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adapters.py import error #11

Closed splaisan closed 4 years ago

splaisan commented 4 years ago

chopchop returns error at runtime when replacing the original adapters.py by the one here the error occurs when trying to import make_full_rapid_barcode_adapter which has been moved to make_new_full_rapid_barcode_adapter in the replacement adapters.py

should we simply rename it and remove new_ or is there more to do here?

Thanks

SorenKarst commented 4 years ago

Hi Stephane,

The format of the adapters.py have changed with the new version of porechop. I have made a fix for this in the developer version of the pipeline https://github.com/SorenKarst/longread-UMI-pipeline/tree/develop . This will become an official release early January.

Let me know if this does not fix the problem for you.

regards Søren

splaisan commented 4 years ago

Thanks Søren I have made a customized version of the main script to allow using other primers and other cutoffs and it finally seems to work.

I will look at your new version when it becomes the main branch and adapt my code

Thanks for the great suite of commands

PS: hope the conda yaml config file from @mdehollander is also part of your next release, it was for me of great help to install the proper versions of the dependencies.