Peter Vegh

Thanks for the clarification and correction. I'll have a look into this method and test it.

I tested the fragments with [CUBA](https://cuba.genomefoundry.org/simulate_gg_assemblies) and can confirm that annotations that overlap with an overhang are lost. This was tested using added annotations that span or partially overlap with...

Thanks for the feedback & the patience, I'm currently updating it to work on Python 3.9, but the latest biopython causes an issue with BioBrickStandardAssembly (there is an extra B'...

Thanks for your interest! Indeed the next project on our list is to update CUBA to the latest front-end packages and EGF Python packages. May I ask your use-case? The...

A solution for linear assembly, using oligos, can be found here: https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/issues/14#issuecomment-1138371834

What command did you run? I have never come across this problem (or appdirs). I had no problem building CUBA now from scratch on Ubuntu (18.04), with `docker-compose build --no-cache`....

Just to add a comment, if you don't have the parts already (as sequence files / in the freezer) and you do a 1-level assembly, then you can also use...

CAB is a boilerplate software and the default parameters should be changed. This said, I don't think the corresponding 3 lines are required: https://github.com/Edinburgh-Genome-Foundry/CAB/blob/b8abbae20038012cd2f44af26be157fd37ae83c2/backend/Dockerfile#L10 In any case I'm updating CUBA...

Thanks for trying out this tool. Indeed, `join()` Genbank features are translated into one feature with the first start and last end locations. In detail, `.translate_record("plasmid.gb")` calls `dna_features_viewer.biotools.load_record()` which returns...

There may also be room for code improvement: `BiopythonTranslatorBase.translate_record()` calls `self.compute_filtered_features()` but this is defined only in the child class `BiopythonTranslator`. Proposed solution is to move `compute_filtered_features()` to the parent...