Hi Pygr-dev, I have been using jbrowse[1] to render tracks and it's really nice. The tracks are handled through an AJAX exchange of NCLists. The jbrowse paper[2] states:
"The JBrowse server requires some preprocessing of tracks before they can be served to the client (see the Methods section for details); Perl scripts to do this preprocessing are provided. Feature tracks are stored in Nested Containment Lists (NCLists) (Alekseyenko and Lee 2007), gene names and other text-navigable labels are stored in Patricia tries (Morrison 1968), and quantitative (wiggle) tracks are rendered as image files. The preprocessing outputs are stored as static files on the server; these files can then be served with minimal server load and they can also be cached by the user's web browser to reduce subsequent data traffic." Unfortunately, the perl scripts for generating the JSON encoding of the NCList are based on GFF3 parsing of BioPerl, which fail for even simple text cases[3] and go out of memory for real data. It would be much nicer if I could serialize the NCLists from pygr into this format, giving me a super cool interface based on pygrs solid data management. So can anyone comment if this approach is sensible and possible? Extra points for sketching the details of an implementation ;) [1] http://jbrowse.org/ [2] http://genome.cshlp.org/content/19/9/1630.full [3] http://old.nabble.com/filter_by_location-in-Bio::DB::SeqFeature::Store::memory-td27170383.html James -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-...@googlegroups.com. To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en.
