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 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
