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

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 <[email protected]> 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 <[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
> >
> > _______________________________________________
> > Biopython mailing list  -  [email protected]
> > https://mailman.open-bio.org/mailman/listinfo/biopython
>

_______________________________________________
Biopython mailing list  -  [email protected]
https://mailman.open-bio.org/mailman/listinfo/biopython