[Biopython] Converting transcript coordinates to genome coordinates

[Peter Cock]

Hopefully Lenna might be willing to take on that role?

Peter

On Mon, Jul 10, 2017 at 3:24 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> 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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