Help with SCENIC+

Question

[Chris]

Hi Biostars,

I try to run SCENIC + tutorial and had error at this cell:

from scenicplus.wrappers.run_pycistarget import run_pycistarget
run_pycistarget(
    region_sets = region_sets,
    species = 'homo_sapiens',
    save_path = os.path.join(work_dir, 'motifs'),
    ctx_db_path = rankings_db,
    dem_db_path = scores_db,
    path_to_motif_annotations = motif_annotation,
    run_without_promoters = True,
    n_tpu = 1,
    _temp_dir = os.path.join(tmp_dir, 'ray_spill'),
    annotation_version = 'v10nr_clust',
    )
AssertionError                            Traceback (most recent call last)
Input In [61], in <cell line: 2>()
      1 from scenicplus.wrappers.run_pycistarget import run_pycistarget
----> 2 run_pycistarget(
      3     region_sets = region_sets,
      4     species = 'homo_sapiens',
      5     save_path = os.path.join(work_dir, 'motifs'),
      6     ctx_db_path = rankings_db,
      7     dem_db_path = scores_db,
      8     path_to_motif_annotations = motif_annotation,
      9     run_without_promoters = True,
     10     n_tpu = 1,
     11     _temp_dir = os.path.join(tmp_dir, 'ray_spill'),
     12     annotation_version = 'v10nr_clust',
     13     )

File /apps/software/jupyter/python_3.9/lib/python3.9/site-packages/scenicplus/wrappers/run_pycistarget.py:182, in run_pycistarget(region_sets, species, save_path, custom_annot, save_partial, ctx_db_path, dem_db_path, run_without_promoters, biomart_host, promoter_space, ctx_auc_threshold, ctx_nes_threshold, ctx_rank_threshold, dem_log2fc_thr, dem_motif_hit_thr, dem_max_bg_regions, annotation, motif_similarity_fdr, path_to_motif_annotations, annotation_version, n_cpu, _temp_dir, exclude_motifs, exclude_collection, **kwargs)
    180 ## CISTARGET
    181 regions = region_sets[key]
--> 182 ctx_db = cisTargetDatabase(ctx_db_path, regions)  
    183 if exclude_motifs is not None:
    184     out = pd.read_csv(exclude_motifs, header=None).iloc[:,0].tolist()

File /apps/software/jupyter/python_3.9/lib/python3.9/site-packages/pycistarget/motif_enrichment_cistarget.py:67, in cisTargetDatabase.__init__(self, fname, region_sets, name, fraction_overlap)
     48 def __init__(self, 
     49             fname: str,
     50             region_sets: Union[Dict[str, pr.PyRanges], pr.PyRanges] = None,
     51             name: str = None,
     52             fraction_overlap: float = 0.4):
     53     """
     54     Initialize cisTargetDatabase
     55     
   (...)
     65         Minimal overlap between query and regions in the database for the mapping.     
     66     """
---> 67     self.regions_to_db, self.db_rankings, self.total_regions = self.load_db(fname,
     68                                                       region_sets,
     69                                                       name,
     70                                                       fraction_overlap)

File /apps/software/jupyter/python_3.9/lib/python3.9/site-packages/pycistarget/motif_enrichment_cistarget.py:110, in cisTargetDatabase.load_db(self, fname, region_sets, name, fraction_overlap)
    108 if name is None:
    109     name = os.path.basename(fname)
--> 110 db = FeatherRankingDatabase(fname, name=name)
    111 total_regions = db.total_genes
    112 db_regions = db.genes

File /apps/software/jupyter/python_3.9/lib/python3.9/site-packages/ctxcore/rnkdb.py:106, in FeatherRankingDatabase.__init__(self, fname, name)
     98 """
     99 Create a new feather database.
    100 
    101 :param fname: The filename of the database.
    102 :param name: The name of the database.
    103 """
    104 super().__init__(name=name)
--> 106 assert os.path.isfile(fname), """Database "{fname}" doesn't exist."""
    108 self._fname = fname
    109 self.ct_db = CisTargetDatabase.init_ct_db(
    110     ct_db_filename=self._fname, engine="pyarrow"
    111 )
    AssertionError: Database "{fname}" doesn't exist.

I downloaded 3 files that requires:

rankings_db = os.path.join(db_fpath, 'cluster_SCREEN.regions_vs_motifs.rankings.v2.feather')
scores_db =  os.path.join(db_fpath, 'cluster_SCREEN.regions_vs_motifs.scores.v2.feather')
motif_annotation = os.path.join(motif_annot_fpath, 'motifs-v10-nr.hgnc-m0.00001-o0.0.tbl')

• https://scenicplus.readthedocs.io/en/latest/pbmc_multiome_tutorial.html#Tutorial:-10x-multiome-pbmc
• https://github.com/aertslab/scenicplus/issues/69

Would you please have a look? Thank you so much!

Answer 1

[corbettberry]

I suspect you saved your .feather and your .tbl as different names than what was included in the tutorial. Hope that helps!