Open Jay2942023 opened 10 months ago
Here is the error:
File "/usr/local/lib/python3.8/site-packages/pycistarget/motif_enrichment_dem.py", line 319, in init
self.run(dem_db.db_scores, **kwargs)
File "/usr/local/lib/python3.8/site-packages/pycistarget/motif_enrichment_dem.py", line 365, in run
region_groups = [create_groups(contrast = contrasts[x],
File "/usr/local/lib/python3.8/site-packages/pycistarget/motif_enrichment_dem.py", line 365, in
Hi @Jay2942023
Can you check wether the chromosome names in your sets of regions map with the chromosome names in the genome annotation (pr_annot
).
All the best,
Seppe
Hi @SeppeDeWinter
I am encountering the same 'ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements' on this code chunk
for DAR in markers_dict.keys(): regions = markers_dict[DAR].index[markers_dict[DAR].index.str.startswith('chr')] region_sets['DARs'][DAR] = pr.PyRanges(region_names_to_coordinates(regions))
my annot has following chromosome names: ` Chromosome | Start | Strand | Gene | Transcript_type |
---|---|---|---|---|
chr2 | 154551776 | 1 | Actl10 | protein_coding |
chrX | 31117674 | 1 | Btbd35f29 | protein_coding |
chr7 | 84915781 | 1 | Olfr290 | protein_coding |
chrY | 90839177 | -1 | Gm21748 | protein_coding |
chr4 | 108719649 | 1 | 3110021N24Rik | protein_coding |
... | ... | ... | ... | ... |
chr6 | 134791334 | -1 | Dusp16 | protein_coding |
chr14 | 51203391 | 1 | Ear14 | protein_coding |
chr14 | 51203689 | 1 | Ear14 | protein_coding |
chr12 | 85274286 | 1 | Zc2hc1c | protein_coding |
chr12 | 85288591 | 1 | Zc2hc1c | protein_coding |
`
and my markers_dict has following chromosome details: `{'AP, cycling': Log2FC Adjusted_pval Contrast chr1:146160518-146161018 2.952461 6.024392e-25 AP, cycling chr18:33138394-33138894 2.950420 5.393040e-25 AP, cycling chr2:120537711-120538211 2.950420 5.393040e-25 AP, cycling chr1:64330705-64331205 2.906402 5.527621e-25 AP, cycling chr7:125731094-125731594 2.904940 6.708995e-25 AP, cycling ... ... ... ... chr15:10746557-10747057 0.586071 2.838126e-08 AP, cycling chr7:89400669-89401169 0.586049 8.302689e-14 AP, cycling chr17:23726623-23727123 0.585742 3.541455e-20 AP, cycling chr8:54724231-54724731 0.585447 2.128771e-21 AP, cycling chr6:120471574-120472074 0.585394 3.926210e-09 AP, cycling
[11247 rows x 3 columns], 'BP, neurogenic': Log2FC Adjusted_pval Contrast chr12:52020608-52021108 4.009526 1.576404e-79 BP, neurogenic chr2:96499436-96499936 3.983610 1.576404e-79 BP, neurogenic`
Could you please help me fix this error? Thanks
Hello,
I am trying to get familiar with SCENIC+ workflow using 10x multiome pbmc tutorial. However, pycistarget couldn't generate menr.pkl file for SCENIC+ input. All I get are a few lists of html file for different topics. Here I attached the code and error message.
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_cpu = 8, _temp_dir = os.path.join(tmp_dir, 'ray_spill'), annotation_version = 'v10nr_clust', )