3.0 years ago by
That is brains exploding level of genius. I'm glad I stole the SICER rewrite away from you so you could come up with this :)
Various ideas in random order (the list will probably grow):
Making UCSC tracks easy to discover and include would be neat, like for example if you know you want to display all tracks from UCSC from the HaCaT cell line you could easily do it with a regex, like
java asciigenome mytrack.bigwig --ucsc '*hacat*' # displays my track, and some HaCaT ones from UCSC
(You could probably think of a better CLI than the one suggested above.)
Perhaps a UCSC command line track downloader/getter is a good idea on its own?
Is it possible to write the "images" to a regular text file? If not, that would be a neat option.
Would be nice if the user could supply a gene track and get the distance to to the nearest gene (in each direction) on a line on the bottom together with the names of any genes overlapping with the currently viewed region. If I want to view regions from a TF chip-seq experiment it would be nice to know which genes are close.
Can arbitrarily many tracks be viewed? I have a time series experiment with ten timepoints and would love to view some regions with all times on top of each other.
It would be great if I could input a file of regions I want displayed and have them all saved in one big pdf/png. After ChIP-Seq experiments I am left with a few hundred regions I want to look more closely at. It would be nice I could just input one file with these regions together with a bigwig/bedgraph and
asciigenome would create one big report that I could scroll through afterwards. It would be nice if asciigenome also could allow the user to give each region included in the report a name and a description like:
# label, organism, assembly, chromosome, start, end, description, upstream, downstream
IL10, human, hg18, chr1, 205007571, 205012462, "involved in immunity", 10000, 1000
PRNP, human, hg18, chr20, 4615157, 4630234, "Prion Protein", 10000, 10000
HSPB4, human, hg18, chr21, 43462210, 43465982, "Heat-shock protein", 10000, 10000
See the example report here: http://bioinfoblog.it/2011/12/a-script-to-fetch-images-from-the-ucsc-browser/
Ps. will start to use this tomorrow as I hate GUIs/the mouse.