[BioPython] retrieve sequence coordinates of exons for a stretch of genes

[Tiago Antão]

On Thu, Feb 14, 2008 at 6:02 AM, Kevin Lam <ULNJUJERYDIX at spammotel.com> wrote:
>  I have been scouring through the web for something I thought was a rather
>  simple task but I can't find the answer.
>
>  How do I get the sequence coordinates for exons of genes in a stretch of
>  genome demarcated by say HoxA13 and Hox A1 ?
>
>  below is the example of the data I am looking for.
>
>  1026087..1026688    1026807..1026834    1026839..1027045    HOXD12
>  1033641..1034421    1035192..1035427    1035428..1035873    HOXD11

Have a look at the UCSC Genome Browser
http://genome.cse.ucsc.edu/cgi-bin/hgTables
on the table knownGene you have things like lists of exonStarts and exonEnds.

I would like, in the long run, to support this in biopython (I have
python code which I can share), but this won't happen in the next few
months for sure (unless it is some sort of team work...).