Peter Vegh

Yes, where there is strandedness, the annotation entry will look something like `'molecule_type': 'ss-tRNA'`. Ok, I'll try and implement (1).

Perhaps subclassing `ProgressLogger` (or `ProgressBarLogger`) and overwriting `callback()` (or `bars_callback()`) as instructed here https://github.com/Edinburgh-Genome-Foundry/Proglog/blob/a30940710bdd52cebc65491984657ad26eca8365/proglog/proglog.py#L49 and [here](https://github.com/Edinburgh-Genome-Foundry/Proglog/blob/a30940710bdd52cebc65491984657ad26eca8365/proglog/proglog.py#L210) is the answer to this? Then you can instruct it to print using your...

Thanks for posting the code. What do you have in mind for valid record picking? One option I can think of is filtering by expected length (maybe using the sizes...

I have looked into this recently as I realised the newer Snapgene versions do not output a correct genbank format (even using 'Genbank - Standard' export). An old version of...

Thanks for looking into this. The change alone won't work, because this code is also run: https://github.com/biopython/biopython/blob/dda590d43f7b09eecab40982a4c1ac9fd49fc3b6/Bio/GenBank/__init__.py#L847 Agreed that checking for "NA" alone will allow 33NA etc, however, this weakness...

Thanks for the contribution. I wouldn't add DFV by default as it's too heavy and not needed for the core functionalities. Crazydoc [does handle a missing DFV](https://github.com/Edinburgh-Genome-Foundry/crazydoc/blob/master/crazydoc/plots.py#L23), but I can...

Thank you, actually it's a new property: https://biopython.org/docs/1.81/api/Bio.Seq.html and has been addressed in https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/pull/79 My solution would be to update Biopython (and Python as support for 3.6 ended a while...

Thank you. The issue seems to arise when the csv is terminated with an empty line, which is common and probably a preferable format as well. I'll address this later...

Thank you -- it's now addressed in above merged PRs.

Hi, `AvoidChanges` should be sufficient in itself, shortly, as a constraint it will keep the sequence or fail. Note it can be used as an objective too, but that does...