Hard-coded paths to files

[anamariaelek]

Hi,

I tried running your pipeline on my data, and I stumbled across some hard-coded paths in the code, e.g.

process_cluster.py line 69 pointing to /home/jvierstra/data/motifs/cluster/20181012/all.dbs.meme, a file with all motifs in meme format

viz_cluster.py line 59 pointing to /home/jvierstra/data/motifs/moods/GRCh38_no_alts.alldbs.1e-4/pfm/, what I reckon should be plain matrices (as used by MOODS)?

I worked around this by modifying the scripts, but it would be nice if these paths could be passed as arguments.

Best regards

[jvierstra]

Thanks for pointing this out -- will get to this as soon as I have time.

[anamariaelek]

Another related file that I am trying to recreate is: /home/jvierstra/proj/code/motif-clustering/tomtom/height.0.70/cluster-info.with.dbd.and.color.csv in Do you add DBDs and colours manually to all clusters there?

Thank you for putting up this amazing resource!

[jvierstra]

Yes. These were added manually.