loosolab/TF-COMB

Kernal crashing at get_pair_locations

Opened this issue · 3 comments

annrosebright commented

Hi,

Thank you for generating this great tool. I am having an issue while running the following step:
pairs = Ce16.get_pair_locations(("TCF4_1","NFIB_1"))

The kernel is always crashing and I am not able to understand what the problem is. Could you suggest some way I could identify the issue or have a workaround to get the location of regions where certain pairs of TFs are present?

Thanks a lot in advance.
Best,
Ann

msbentsen commented

Hi Ann,

Can you try it with the TF-COMB from the development branch by installing:
pip install git+https://github.com/loosolab/TF-COMB@dev

The version (1.0.4) is not released yet, but I believe we solved a bug related to this. I hope that solves the issue!

annrosebright commented

Thanks a lot, it worked.

Another question: is there a way to manage the pdf size while using:
Ce16.plot_TFBS(window_chrom = "chr9",
window_start = 73935027,
window_end = 73935159,
fasta="/datastore_share/Users/ann/genome/GRCm38.p6.genome.fa",save = "Chr9_NFIB_TCF4.pdf", TFBS_track_height=6)

I can manage the track height but can i manage the width of the track or pdf as well?

Thank you.

msbentsen commented

I can manage the track height but can i manage the width of the track or pdf as well?

Good question - I realized there was no method for this, so I just added the option "figsize" to the new version TF-COMB=1.1. There is an example here:
https://tf-comb.readthedocs.io/en/latest/examples/plot_TFBS_genome_view.html#Set-figsize-to-control-size-of-plot-(the-default-is-to-estimate-it-from-the-number-of-tracks)
which shows how to use it to control the final size of the figure, so then you can adjust until it is right.

So yes, if you just update the version, that should be available!