Hello Martin,
There is a utility in the kent source tree that you can use to re-order
a maf file:
$ mafOrder
mafOrder - order components within a maf file
usage:
mafOrder mafIn order.lst mafOut
where order.lst has one species per line
How to get the kent source tree:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
Please feel free to contact the mailing list support team again if you
would like more assistance.
Warm regards,
Jen
UCSC Genome Browser Support
On 8/10/10 12:04 AM, Martin A. Smith wrote:
> Esteemed colleagues,
>
> I was wondering if there is an existing tool that sorts a group of maf
> blocks with respect to some specie's coordinates. In other words, I
> would like to reorder a MSA with reference species X to reference
> species Y and upload it as a custom track for database Y.
>
> Kind regards,
>
> Martin Smith
> PhD Student
> Institute for Molecular Bioscience
> University of Queensland
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