[Biopython] writing cut sites in genbank via biopython

[Jocelyne]

Hi Peter,

Thank you so much for always being so helpful. You're correct, that was my
issue. Thank you again!

Jocelyne

On Wed, Oct 7, 2020 at 1:27 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 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 <jocelyne at gmail.com> 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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> > https://mailman.open-bio.org/mailman/listinfo/biopython
>
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