cli pyscenic ctx error [BUG] #275
Description
I am trying to run CLI pcyscenic ctx, and have run into some problems. Once I added no_pruning, the tool ran for a while, but had the following error.
Steps to reproduce the behavior
- Command run when the error occurred:
pyscenic ctx test.tsv \
data/feather_databases/mm9-500bp-upstream-10species.mc9nr.feather data/feather_databases/mm9-500bp-upstream-7species.mc9nr.feather data/feather_databases/mm9-tss-centered-10kb-10species.mc9nr.feather data/feather_databases/mm9-tss-centered-10kb-7species.mc9nr.feather data/feather_databases/mm9-tss-centered-5kb-10species.mc9nr.feather data/feather_databases/mm9-tss-centered-5kb-7species.mc9nr.feather \
--annotations_fname data/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \
--expression_mtx_fname data/dge.1.MG.csv \
--output reg.csv \
--mask_dropouts \
-t \
--no_pruning
...
- Error encountered:
Traceback (most recent call last):
File "/home/russell/miniconda3/envs/scenic/bin/pyscenic", line 8, in <module>
sys.exit(main())
File "/home/russell/miniconda3/envs/scenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 485, in main
args.func(args)
File "/home/russell/miniconda3/envs/scenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 191, in prune_targets_command
df_motifs = calc_func(dbs, modules, motif_annotations_fname,
File "/home/russell/miniconda3/envs/scenic/lib/python3.8/site-packages/pyscenic/prune.py", line 379, in find_features
return add_motif_url(prune2df(rnkdbs, signatures, motif_annotations_fname,
File "/home/russell/miniconda3/envs/scenic/lib/python3.8/site-packages/pyscenic/utils.py", line 326, in add_motif_url
df[("Enrichment", COLUMN_NAME_MOTIF_URL)] = list(map(partial(urljoin, base=base_url), df.index.get_level_values(COLUMN_NAME_MOTIF_ID)))
TypeError: urljoin() got multiple values for argument 'base'
...