[Biopython] Converting transcript coordinates to genome coordinates

[Michiel de Hoon]

Thanks everybody for your replies. I think Lenna's code would work best, and I agree with Peter that it would be good to have this functionality included in Biopython.I could get Lenna's code to work with transcript positions (i.e. cmap.c2g(position)), but as far as I can tell it currently does not handle ranges, i.e. cmap.c2g([start, end]), which gets tricky if the range spans an exon-exon boundary. 
Her code looks well-written, with plenty of test cases, however I feel that the module would need a dedicated maintainer for it to be viable long-term in Biopython.

Thanks again,-Michiel 

    On Thursday, July 6, 2017 7:22 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
 

 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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