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janka2012 / digIS

Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes
MIT License
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Error: Bio.Alphabet has been removed from Biopython #8

Open bersand1 opened 2 months ago

bersand1 commented 2 months ago

As a premise I have a very poor background in informatic and bioinformatic. However for my current research I wanted to test digIS which could satisfiy perfectly my needs.

I was running a genome sequence ( fasta file) without the gene_bank annotation. I followed the instruction and everything was fine until this error

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

Is there something I can do on my side? It seems that the script shoudl be modified.

I would appreciate any type of suggestion

Thank you for your attention Best, Davide

pengxyii commented 1 month ago

Hello, I encountered the same issue as you did. Have you found a solution? Your response would be greatly appreciated.