The script "prep_manual_review.py" tries to imports a function that does not exist in "sequence_record_functions_PIPE"

ArifaKhanLab / RVDB

A reference viral database (RVDB)

https://rvdb.dbi.udel.edu/

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The script "prep_manual_review.py" tries to imports a function that does not exist in "sequence_record_functions_PIPE" #3

Closed onabluemoon closed 5 years ago

onabluemoon commented 5 years ago

I am following the instructions to update RVDB and I have reached the point where I should run the "prep_manual_review.py" script, however this script requires importing a function from "sequence_record_functions_PIPE" that does not exist either in the provided version of this file nor in any version that can be found on your git.

File "prep_manual_review.py", line 5, in from sequence_record_functions_PIPE import get_filenames as getfns ImportError: cannot import name get_filenames

ArifaKhanLab commented 5 years ago

The path of library is updated. Please re-install the pipeline with the updated scripts.

JonathonMifsud commented 3 years ago

Hi, sorry to comment on a closed issue but I am running into a similar problem with RVDB_characterization.py on Linux

Traceback (most recent call last): File "./scripts/RVDB_characterization.py", line 354, in <module> from sequence_record_functions_PIPE import get_accs_flatfile as getaccs ImportError: No module named sequence_record_functions_PIPE

Any suggestions would be greatly appreciated!

ArifaKhanLab commented 3 years ago

Hi JonathonMifsud,

Can you please confirm that you are running Python 2?

JonathonMifsud commented 3 years ago

Thank you for the reply, yes I am running the script with Python2. It looks like the error was my fault and down to a pathing problem to the additional scripts.