cisTarget problem on the FeatherRankingDatabase command

[farhad-zare]

Hi

I just start learning how to work with pyscenic. As a newbie, I was trying to run the tutorial for pyscenic for mice (https://pyscenic.readthedocs.io/en/latest/tutorial.html). However, I received an error related to the command RankingDatabase (FeatherRankingDatabase ). It asks to convert v1 to v2, and when I convert the data and run the command again I got the following error: command: dbs = [RankingDatabase(fname=fname, name=name(fname)) for fname in db_fnames]

Error: cisTarget database filename "/Users/Untitled Folder/mm9-tss-centered-10kb-10species.mc9nr.feather" does not end with ".((motifs|tracks)vs(regions|genes)|(regions|genes)vs(motifs|tracks)).(scores|rankings).feather".

[1833631038]

Did you solve it？

[ghuls]

The file needs to be named: mm9-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather (the last part of the filename needs to end with genes_vs_motifs.rankings.feather.

The databases can be found now on the resources webserver:

https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather

The index page on https://resources.aertslab.org/cistarget/ is not updated yet, but you can navigate to: https://resources.aertslab.org/cistarget/databases/ and download only databases which end with *.rankings.feather

[mpiersonsmela]

I had the exact same problem. I will try downloading https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc9nr/gene_based/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather and see if it works.

You really should update the index page, I wasted a lot of time before finding this.

[ghuls]

Databases in Feather v2 format can be navigated at: https://resources.aertslab.org/cistarget/databases/

[ghuls]

pySCENIC v0.12.0 is out: https://pypi.org/project/pyscenic/. https://resources.aertslab.org/cistarget/databases/ is updated too.