how to import gene annotation in higlass-python

[LiuJie1117]

Hello,

I am trying to visualize my Micro-C data using HiGlass(v1.3.3) with Jupyter Lab. According to https://docs.higlass.io/data_preparation.html#gene-annotation-tracks, I generated a gene-annotations-${ASSEMBLY}.db for dm6 genome. However, I have no idea how to import it in python.

I found examples below, so I thought I should use specific function in higlass to read in it, like hg.cooler for .mcool files or hg.remote for remote tileset.

import higlass as hg

tileset_cooler        = hg.cooler("./test.mcool")

mm10 = hg.remote(
    uid="QDutvmyiSrec5nX4pA5WGQ",
    server="//higlass.io/api/v1",
)

hg.view(
    tileset_cooler.track("horizontal-heatmap", height=300),
    mm10.track("gene-annotations", height=150).opts(minHeight = 24,)
)

So I test:

import higlass as hg
dm6 = hg.annotations("./gene-annotations-dm6.db")

And it failed with TypeError: '_Feature' object is not callable.

So are there any suggestions on how to load in the gene-annotations-${ASSEMBLY}.db file? Or I should generate gene-annotation track in other ways?

Thank you very much!

[LiuJie1117]

I fixed the problem. It should be loaded in with hg.beddb() :)