[Biopython] Converting transcript coordinates to genome coordinates

[Lenna Peterson]

I am willing (and available, now that I've finished my PhD!) to work on
getting the code into the main branch. The main barrier is that I am not
familiar with the finer details of sequence coordinates, so I would benefit
from guidance from a sequence expert for adding missing functionality.

Lenna

On Jul 10, 2017 11:14 AM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> 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
> >>
> >>
> >> _______________________________________________
> >> Biopython mailing list  -  Biopython at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biopython
> >>
> >>
> >> --
> >> Gerard C.P. Schaafsma
> >> Protein Structure and Bioinformatics Group
> >> Dept. of Experimental Medical Science
> >> Lund University
> >> BMC B13, Hs 66
> >> 221 84 Lund
> >> Sweden
> >
> >>
> >>
> >> _______________________________________________
> >> Biopython mailing list  -  Biopython at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biopython
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170720/dce3b258/attachment.html>