TypeError: unbound method set.union() needs an argument

[Melody-cell]

Hi, @SeppeDeWinter ，
when i run "scenicplus prepare_data prepare_menr", it appears this error:

I have checked other people's issues, but i still didn't solve it.
This is my dem_results.html,

Did anyone know how to solve it?

[SeppeDeWinter]

Hi @Melody-cell

Did you check wether one (or more) of your cistromes is empty?

Like I mentioned in:
#470

All the best,

Seppe

[Melody-cell]

Hi, @SeppeDeWinter ,
i checked it , it's not empty.

[Melody-cell]

Hi, @SeppeDeWinter
I saw it in dem_results.hdf5, this is my code:

This is cistromes and region_set:

like this:

[SeppeDeWinter]

Hi @Melody-cell

Ok thanks for checking.
Could you run the following code to see where things are going wrong

from scenicplus.data_wrangling.cistarget_wrangling import (_signatures_to_iter, _get_cistromes)

paths_to_motif_enrichment_results = <PATH_TO_MOTIF_ENRICHMENT_RESULTS> # this is the `--paths_to_motif_enrichment_results` of the `prepare_menr` command
mdata = mudata.read(<PATH_TO_MUDATA>)
scplus_regions = set(mdata["scATAC"].var_names)
direct_annotation = ["Direct_annot"]
extended_annotation: = ["Orthology_annot"]

cistromes = []
for motif_enrichment_table, motif_hits in _signatures_to_iter(
    paths_to_motif_enrichment_results):
    cistromes.extend(
        _get_cistromes(
            motif_enrichment_table = motif_enrichment_table,
            motif_hits = motif_hits,
            scplus_regions = scplus_regions,
            direct_annotation = direct_annotation,
            extended_annotation = extended_annotation))

for cistrome in cistromes:
    if len(cistrome.target_regions) == 0:
        print(cistrome)

[Melody-cell]

Hi, @SeppeDeWinter ,
This is my results:

[SeppeDeWinter]

And does this

union_target_regions= list(set.union(
            *[cistrome.target_regions for cistrome in cistromes]))

produce the error you ware facing? If not, can you also try with the ctx_results.hdf5 file?

Best,

S

[Melody-cell]

Hi, @SeppeDeWinter ,
it produced the error i'm facing. It seems that the cistromes is empty:

In this case, what can i do to solve it?

[Melody-cell]

Hi, @SeppeDeWinter ,
but why cistromes was empty? I don't know where was wrong.

[SeppeDeWinter]

Hi @Melody-cell

This means something went wrong during the motif enrichment step.
Could you check your cistarget database (are you using the correct database?) and the region sets used to run motif enrichment analysis (do they overlap with the database).

Best,

S

[Melody-cell]

Hi, @SeppeDeWinter , i am curious about that why this will appear NaN in the cell data , this means RNA_barcodes not matched completely with ATAC barcodes? but multiome data should be completely match cause they have the same cells. i am confused.