Good Morning Mark:
Have you tried using the public MySQL server ?
http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29
e.g. to see all track information:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
-e "select * from trackDb;" hg19
--Hiram
----- Original Message -----
From: "Mark Dumas" <[email protected]>
To: [email protected]
Sent: Monday, January 16, 2012 4:01:01 AM
Subject: [Genome] dynamic access do ucsc and encode annotation-tracks
Hello,
I would like to access genome-annotation tracks as well as encode data-tracks
from within a python-tool that I am developing.
(My interest is in basepair-positions of the respective annotations, no
sequences needed.)
My question is how I could request the server for a list of the currently
held genome-assemblies and their respective annotation-tracks in a
dynamical way.
For example the user of my tool would select an organism, an assembly and
finally an encode data-track of his interest.
Therefore I would need to get a list of Encode data-tracks and their detailed
description.
The tool would then need to process the position-data of the
gene-annotations as well as the encode data-track on a whole-genome
scale.
Developing in python I can't use the perl-API here.
The best way I found so far would be via the DAS-server, which would give me
the assemblies from
http://genome.cse.ucsc.edu/cgi-bin/das/dsn
and (for example) data-tracks from:
http://genome.cse.ucsc.edu/cgi-bin/das/hg19/types
My problem here is that I do not get a description string describing the
nature of the different encode-tracks obtained via "types".
Also their category is always "other", so I couldn't distinguish encode-tracks
from others.
What would be the query to obtain the list of encode-tracks including a
meaningful description of of what they are.
Also given that I have to work on a whole-genome-scale the DAS-server is
most likely not the best way of getting the whole annotation-tracks in
the end.
What would be the best way ... for getting the list of current tracks and then
for finally getting to the data for processing ?
Thanks a lot for help :-)
Arno
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
