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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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Can't load LOLAExt with loadRegionDB() #10

Closed enricoferrero closed 7 years ago

enricoferrero commented 8 years ago

Hello,

Thanks for LOLA! It looks like a great resource.

I get this error when trying to load the latest LOLAExt cached database:

> regionDB2 <- loadRegionDB("LOLAExt/hg19")
Reading collection annotations:
Error in readCollectionAnnotation(dbLocation, collections) :
  No regions found. Are you sure '../../data/DNase-seq/12LOLA/LOLAExt/hg19' is a region database?
In addition: Warning messages:
1: In readCollectionAnnotation(dbLocation, collections) :
  jaspar_motifs has no collection annotation or region files. Skipping...
2: In readCollectionAnnotation(dbLocation, collections) :
  roadmap_epigenomics has no collection annotation or region files. Skipping...

LOLACore loads fine.

Thanks, Enrico

enricoferrero commented 8 years ago

To fix this it is sufficient to include a collection.txt file in roadmap_epigenomics and jaspar_motifs similar to those used in LOLACore (e.g.: I modified the one from encode_tfbs).

nsheff commented 8 years ago

Thanks for reporting this; I haven't had time to confirm but it should be an easy fix. I'll keep you posted...

nsheff commented 7 years ago

I finally fixed this in the released version; I also fixed a bug in the motif calculation that made the jaspar collection bad. Please update to the latest LOLAExt.

nsheff commented 7 years ago

(you can download the latest databases here: http://databio.org/regiondb)