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

Oh good - because I had no other ideas to suggest.

Peter

On Wed, Oct 7, 2020 at 10:06 PM Jocelyne <[email protected]> wrote:
>
> 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
>> >
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