[Biopython] Converting transcript coordinates to genome coordinates

[Peter Cock]

Hi all,

A while back Lenna submitted a pull request which should be of interest:

https://github.com/biopython/biopython/pull/309

Documentation:

http://biopython.org/wiki/Coordinate_mapping

Example:

https://gist.github.com/lennax/10600113

Having a fresh set of eyes on this would be great, as there does
seem to be enough interest to finish this and get it added to
Biopython.

Thanks,

Peter

On Thu, Jul 6, 2017 at 10:42 AM, Gerard Schaafsma
<gerard.schaafsma at med.lu.se> wrote:
> Hi,
>
> Did you have a look at https://mutalyzer.nl ? There is a position converter
> in there.
>
> Best,
>
> Gerard
>
>
> On 05/07/17 12:04, Michiel de Hoon wrote:
>
> Dear all,
>
> Does anybody have some code to convert transcript coordinates to genome
> coordinates?
> I have the position of a nucleotide along a transcript, and the genome
> coordinates of the start and end of each exon in the transcript, and I would
> like to find the position of the nucleotide in genome coordinates.
> Ideally, I am looking for some code that can find the genome coordinates of
> a sequence of nucleotides.
> For example, if these are the exons:
> exon1  10000 10030
> exon2  10050 10080
> and a nucleotide sequence starting at position 20 and ending at position 50
> in transcript coordinates,
> then I am looking for the genome coordinates (10020,10030), (10050,10070).
>
> Thanks,
> -Michiel
>
>
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>
> --
> Gerard C.P. Schaafsma
> Protein Structure and Bioinformatics Group
> Dept. of Experimental Medical Science
> Lund University
> BMC B13, Hs 66
> 221 84 Lund
> Sweden
>
>
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