Re: [Biopython] writing cut sites in genbank via biopython

I think FeatureLocation(1,1) is correct, but you need to have a record
longer than 1 bp otherwise it gets confused into thinking you have a
feature right at the end of a circular sequence:

https://github.com/biopython/biopython/blob/biopython-178/Bio/SeqIO/InsdcIO.py#L258

Peter

On Wed, Oct 7, 2020 at 7:53 PM Jocelyne <[email protected]> wrote:
>
> Hello,
> I'm trying to write a feature with location "1^2" (a cut site between the first and second base).
>
> If I parse a file that contains a feature with location "1^2", I get back a
> FeatureLocation(ExactPosition(1), ExactPosition(1))
>
> However, if I write a file with `FeatureLocation(ExactPosition(1), ExactPosition(1))` , I get "1^1"
>
> I have tried:
> * FeatureLocation(1,1)   -> 1^1
> * FeatureLocation(1,2)   -> 2
> * FeatureLocation(ExactPosition(1), ExactPosition(1))   -> 1^1
> * FeatureLocation(ExactPosition(1), ExactPosition(2))   -> 2
> * FeatureLocation(FeatureLocation(BetweenPosition(0,0,1), BetweenPosition(1,1,2)))  -> (1^2)..(1^2)
>
> I'm a bit at a loss at this point. Does anyone know how to "1^2" to a genbank file?
>
> Any help is appreciated.
>
> Thank you!
>
> Jocelyne
>
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