Peter Vegh

Results 101 comments of Peter Vegh

I added an improved warning in a more prominent location (in the introductory paragraph), for each relevant class. The Genbank API docs already had a prominent warning. I also added...

Thank you -- I merged the other PR as it's more in line with the ValueError text recommendation. May revisit, depending on further checks.

Thank you for this contribution. I agree it would be useful (cf. https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/issues/47), for example to show features relevant for the negative strand. I'll have to review this in detail...

Thank you for this, yes all features wanted below the track, at least for this issue. I'll add this as an example, perhaps mention in the main readme as well.

If I understand your intention correctly, then I think unfortunately no, it's not possible. Also it will likely be not implemented either, as the key problem this software solves is...

Not sure about the utility, just noticed while looking into another issue. Could be useful for synthetic (xeno) nucleotides. Yes I can try a solution, probably best to do together...

I [implemented a function](https://github.com/Edinburgh-Genome-Foundry/easy_dna/blob/7687fb45eeffa0abca1216fd62ed8d6224ba9d2b/easy_dna/io.py#L374) in one of our packages that checks a Locus line against the strict Genbank format. Now I understand the possible variations of this format and ready...

The best option seems to be to explicitly check whether the whole Molecule Type entry is valid: ``` 48-53 Molecule Type: NA, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA),...

This is not something we do, but there may be a couple of ways to address it. First, setup: you can either download the codebase and install in an editable...

Thanks for the quick reply, yes I can try implementing a solution. There would be a couple of ways to go about it: 1. Check whether there is strandedness in...