Length mismatch: Expected axis has 0 elements, new values have 3 elements #286

Sudheshna30 · 2024-01-17T18:33:28Z

Sudheshna30
Jan 17, 2024

Hi,

I keep getting this error at the run_pysicsTarget step during creating contrast groups may I know why this is happening and how to solve this please?

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[11], line 3
      1 tmp_dir= '/n/holyscratch01/arlotta_lab/Sudheshna/'
      2 from scenicplus.wrappers.run_pycistarget import run_pycistarget
----> 3 run_pycistarget(
      4     region_sets = region_sets,
      5     species = 'mus_musculus',
      6     save_path = os.path.join(work_dir, 'motifs'),
      7     ctx_db_path = rankings_db,
      8     dem_db_path = scores_db,
      9     path_to_motif_annotations = motif_annotation,
     10     run_without_promoters = True,
     11     n_cpu = 1,
     12     _temp_dir = os.path.join(tmp_dir, 'ray_spill'),
     13     annotation_version = 'v10nr_clust',
     14     )

File /n/holyscratch01/arlotta_lab/Sudheshna/scenicplus/src/scenicplus/wrappers/run_pycistarget.py:263, 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)
    261     for col in exclude_collection:
    262         dem_db.db_scores = dem_db.db_scores[~dem_db.db_scores.index.str.contains(col)]
--> 263 menr['DEM_'+key+'_All'] = DEM(dem_db = dem_db,
    264                    region_sets = regions,
    265                    log2fc_thr = dem_log2fc_thr,
    266                    motif_hit_thr = dem_motif_hit_thr,
    267                    max_bg_regions = dem_max_bg_regions,
    268                    specie = species,
    269                    genome_annotation = annot_dem,
    270                    promoter_space = promoter_space,
    271                    motif_annotation =   annotation,
    272                    motif_similarity_fdr = motif_similarity_fdr, 
    273                    path_to_motif_annotations = path_to_motif_annotations,
    274                    n_cpu = n_cpu,
    275                    annotation_version = annotation_version,
    276                    tmp_dir = save_path,
    277                    _temp_dir= _temp_dir,
    278                    **kwargs)
    279 out_folder = os.path.join(save_path,'DEM_'+key+'_All')
    280 check_folder = os.path.isdir(out_folder)

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pycistarget/motif_enrichment_dem.py:319, in DEM.__init__(self, dem_db, region_sets, specie, subset_motifs, contrasts, name, max_bg_regions, adjpval_thr, log2fc_thr, mean_fg_thr, motif_hit_thr, n_cpu, fraction_overlap, cluster_buster_path, path_to_genome_fasta, path_to_motifs, genome_annotation, promoter_space, path_to_motif_annotations, annotation_version, motif_annotation, motif_similarity_fdr, orthologous_identity_threshold, tmp_dir, **kwargs)
    317 self.cistromes = None
    318 if dem_db is not None:
--> 319     self.run(dem_db.db_scores, **kwargs)

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pycistarget/motif_enrichment_dem.py:365, in DEM.run(self, dem_db_scores, **kwargs)
    363 # Get region groups
    364 log.info('Creating contrast groups')
--> 365 region_groups = [create_groups(contrast = contrasts[x],
    366                            region_sets_names = region_sets_names,
    367                            max_bg_regions = self.max_bg_regions,
    368                            path_to_genome_fasta = self.path_to_genome_fasta,
    369                            path_to_regions_fasta = os.path.join(self.tmp_dir, contrasts_names[x] +'.fa'),  
    370                            cbust_path = self.cluster_buster_path,
    371                            path_to_motifs = self.path_to_motifs,
    372                            annotation = self.genome_annotation,
    373                            promoter_space = self.promoter_space,
    374                            motifs = dem_db_scores.index.tolist(),
    375                            n_cpu = self.n_cpu,
    376                            **kwargs) for x in range(len(contrasts))]
    378 # Compute p-val and log2FC
    379 if self.n_cpu > len(region_groups):

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pycistarget/motif_enrichment_dem.py:365, in <listcomp>(.0)
    363 # Get region groups
    364 log.info('Creating contrast groups')
--> 365 region_groups = [create_groups(contrast = contrasts[x],
    366                            region_sets_names = region_sets_names,
    367                            max_bg_regions = self.max_bg_regions,
    368                            path_to_genome_fasta = self.path_to_genome_fasta,
    369                            path_to_regions_fasta = os.path.join(self.tmp_dir, contrasts_names[x] +'.fa'),  
    370                            cbust_path = self.cluster_buster_path,
    371                            path_to_motifs = self.path_to_motifs,
    372                            annotation = self.genome_annotation,
    373                            promoter_space = self.promoter_space,
    374                            motifs = dem_db_scores.index.tolist(),
    375                            n_cpu = self.n_cpu,
    376                            **kwargs) for x in range(len(contrasts))]
    378 # Compute p-val and log2FC
    379 if self.n_cpu > len(region_groups):

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pycistarget/motif_enrichment_dem.py:534, in create_groups(contrast, region_sets_names, max_bg_regions, path_to_genome_fasta, path_to_regions_fasta, cbust_path, path_to_motifs, annotation, promoter_space, motifs, n_cpu, **kwargs)
    532 nr_no_pr = max_bg_regions-nr_pr
    533 # Nr of promoters in the background
--> 534 bg_pr_overlap = pr.PyRanges(region_names_to_coordinates(background)).count_overlaps(annotation)
    535 bg_pr = coord_to_region_names(bg_pr_overlap[bg_pr_overlap.NumberOverlaps != 0][['Chromosome', 'Start', 'End']])
    536 bg_no_pr = coord_to_region_names(bg_pr_overlap[bg_pr_overlap.NumberOverlaps == 0][['Chromosome', 'Start', 'End']])

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pycistarget/utils.py:33, in region_names_to_coordinates(region_names)
     31 regiondf=pd.concat([chrom, start, end], axis=1, sort=False)
     32 regiondf.index=[i for i in region_names if ':' in i]
---> 33 regiondf.columns=['Chromosome', 'Start', 'End']
     34 return(regiondf)

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pandas/core/generic.py:5920, in NDFrame.__setattr__(self, name, value)
   5918 try:
   5919     object.__getattribute__(self, name)
-> 5920     return object.__setattr__(self, name, value)
   5921 except AttributeError:
   5922     pass

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pandas/_libs/properties.pyx:69, in pandas._libs.properties.AxisProperty.__set__()

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pandas/core/generic.py:822, in NDFrame._set_axis(self, axis, labels)
    820 def _set_axis(self, axis: int, labels: AnyArrayLike | list) -> None:
    821     labels = ensure_index(labels)
--> 822     self._mgr.set_axis(axis, labels)
    823     self._clear_item_cache()

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pandas/core/internals/managers.py:228, in BaseBlockManager.set_axis(self, axis, new_labels)
    226 def set_axis(self, axis: int, new_labels: Index) -> None:
    227     # Caller is responsible for ensuring we have an Index object.
--> 228     self._validate_set_axis(axis, new_labels)
    229     self.axes[axis] = new_labels

File ~/miniconda3/envs/scenicplus/lib/python3.9/site-packages/pandas/core/internals/base.py:70, in DataManager._validate_set_axis(self, axis, new_labels)
     67     pass
     69 elif new_len != old_len:
---> 70     raise ValueError(
     71         f"Length mismatch: Expected axis has {old_len} elements, new "
     72         f"values have {new_len} elements"
     73     )

ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 element

SeppeDeWinter · 2024-01-19T17:15:28Z

SeppeDeWinter
Jan 19, 2024
Maintainer

Hi @Sudheshna30

It looks like your background set of regions is empty.
This can occur when there are duplicate region sets, can you check this?

All the best,

Seppe

8 replies

SeppeDeWinter Feb 1, 2024
Maintainer

This is the reason why you were having the issue with motif enrichment analysis.

You'll have to go back to the DAR calculation step and check wether anything went wrong over there. Also 65k are really a lot of regions for a DAR set.

Good luck.

All the best,

Seppe

xwangda Aug 30, 2024

Dear Seppe,
Thank you so much for developing this amazing tool, I have been a user of SCENIC, while I do meet some problems when trying SCENIC+ since I am new to both scATAC analysis and python.
I am also stuck at this step with the same error:

error

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[115], [line 3](vscode-notebook-cell:?execution_count=115&line=3)
      [1](vscode-notebook-cell:?execution_count=115&line=1) for DAR in markers_dict.keys():
      [2](vscode-notebook-cell:?execution_count=115&line=2)     regions = markers_dict[DAR].index[markers_dict[DAR].index.str.startswith('chr')] #only keep regions on known chromosomes
----> [3](vscode-notebook-cell:?execution_count=115&line=3)     region_sets['DARs'][DAR] = pr.PyRanges(region_names_to_coordinates(regions))

File ~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pycistarget/utils.py:35, in region_names_to_coordinates(region_names)
     [33](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pycistarget/utils.py:33) regiondf=pd.concat([chrom, start, end], axis=1, sort=False)
     [34](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pycistarget/utils.py:34) regiondf.index=[i for i in region_names if ':' in i]
---> [35](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pycistarget/utils.py:35) regiondf.columns=['Chromosome', 'Start', 'End']
     [36](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pycistarget/utils.py:36) return(regiondf)

File ~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:5920, in NDFrame.__setattr__(self, name, value)
   [5918](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:5918) try:
   [5919](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:5919)     object.__getattribute__(self, name)
-> [5920](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:5920)     return object.__setattr__(self, name, value)
   [5921](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:5921) except AttributeError:
   [5922](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:5922)     pass

File ~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/_libs/properties.pyx:69, in pandas._libs.properties.AxisProperty.__set__()

File ~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:822, in NDFrame._set_axis(self, axis, labels)
    [820](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:820) def _set_axis(self, axis: int, labels: AnyArrayLike | list) -> None:
    [821](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/generic.py:821)     labels = ensure_index(labels)
...
     [71](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/internals/base.py:71)         f"Length mismatch: Expected axis has {old_len} elements, new "
     [72](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/internals/base.py:72)         f"values have {new_len} elements"
     [73](https://vscode-remote+ssh-002dremote-002b143-002e89-002e53-002e126.vscode-resource.vscode-cdn.net/d1/xinlei/~/anaconda3/envs/scenic+/lib/python3.11/site-packages/pandas/core/internals/base.py:73)     )

ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements

When I checked the region_sets['DARs'] file I found the chromosome profiles were partially overlapped between two cell types, and the rest cell types looks totally different. Could you help to check if my problem was the same as Sudheshna30? Can I solve the problem by combining the two cell types? I would appreciate you time and help, thanks!

# Attached is the region_sets['DARs']
{'B': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 148918298 | 148918684 |
 | chr1         | 111878356 | 111878972 |
 | chr1         | 222798097 | 222798376 |
 | chr1         | 20119205  | 20119762  |
 | ...          | ...       | ...       |
 | chrX         | 109889017 | 109889775 |
 | chrX         | 40468346  | 40468669  |
 | chrX         | 132488338 | 132490175 |
 | chrX         | 53313408  | 53313669  |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 8,717 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'CD14Mono': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 99700069  | 99700344  |
 | chr1         | 223177764 | 223178035 |
 | chr1         | 199742575 | 199742899 |
 | chr1         | 17603348  | 17603704  |
 | ...          | ...       | ...       |
 | chrX         | 123784707 | 123785245 |
 | chrX         | 154368495 | 154369211 |
 | chrX         | 129931161 | 129932976 |
 | chrX         | 40406314  | 40406889  |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 10,877 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'CD16Mono': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 113663078 | 113663442 |
 | chr1         | 10378481  | 10378747  |
 | chr1         | 211908331 | 211908781 |
 | chr1         | 147635352 | 147635702 |
 | ...          | ...       | ...       |
 | chrX         | 41441851  | 41442946  |
 | chrX         | 123859390 | 123860728 |
 | chrX         | 37786455  | 37787832  |
 | chrX         | 79065554  | 79066059  |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 11,279 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'CD3+CD4-CD8-T': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 84876239  | 84876648  |
 | chr1         | 193592294 | 193592722 |
 | chr1         | 210332197 | 210332545 |
 | chr1         | 3810091   | 3810566   |
 | ...          | ...       | ...       |
 | chrX         | 139739060 | 139739522 |
 | chrX         | 124339085 | 124339474 |
 | chrX         | 124063803 | 124064573 |
 | chrX         | 72018150  | 72018933  |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 4,098 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'CytotoxicCD8T': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 53574758  | 53575389  |
 | chr1         | 229194225 | 229194444 |
 | chr1         | 168360163 | 168360430 |
 | chr1         | 7915700   | 7916120   |
 | ...          | ...       | ...       |
 | chrX         | 73214290  | 73215141  |
 | chrX         | 154368495 | 154369211 |
 | chrX         | 40026919  | 40027385  |
 | chrX         | 135383975 | 135384563 |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 6,208 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'DC': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 21815669  | 21816203  |
 | chr1         | 154860353 | 154860819 |
 | chr1         | 19436687  | 19436992  |
 | chr1         | 247639307 | 247639724 |
 | ...          | ...       | ...       |
 | chrX         | 47361644  | 47362414  |
 | chrX         | 65694648  | 65695185  |
 | chrX         | 13081536  | 13081998  |
 | chrX         | 154541981 | 154543312 |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 11,776 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'NK': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 1221863   | 1222184   |
 | chr1         | 157399861 | 157400388 |
 | chr1         | 162411603 | 162412344 |
 | chr1         | 109788279 | 109788532 |
 | ...          | ...       | ...       |
 | chrX         | 123784707 | 123785245 |
 | chrX         | 9351228   | 9352194   |
 | chrX         | 42933948  | 42934833  |
 | chrX         | 72105260  | 72105845  |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 6,056 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'NaiveCD4T': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 24475663  | 24475981  |
 | chr1         | 181423457 | 181423874 |
 | chr1         | 44305897  | 44306508  |
 | chr1         | 59892761  | 59893688  |
 | ...          | ...       | ...       |
 | chrX         | 17736760  | 17738417  |
 | chrX         | 103310112 | 103311226 |
 | chrX         | 65034247  | 65035549  |
 | chrX         | 131740900 | 131742185 |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 4,526 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'NaiveCD8T': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 24475663  | 24475981  |
 | chr1         | 181423457 | 181423874 |
 | chr1         | 44305897  | 44306508  |
 | chr1         | 53986212  | 53986795  |
 | ...          | ...       | ...       |
 | chrX         | 73977303  | 73977964  |
 | chrX         | 38560849  | 38561669  |
 | chrX         | 135342835 | 135343070 |
 | chrX         | 47380046  | 47380653  |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 3,730 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.,
 'Neutrophil': +--------------+-----------+-----------+
 | Chromosome   | Start     | End       |
 | (category)   | (int32)   | (int32)   |
 |--------------+-----------+-----------|
 | chr1         | 51666524  | 51666867  |
 | chr1         | 166511781 | 166512084 |
 | chr1         | 162234976 | 162235447 |
 | chr1         | 58618285  | 58618675  |
 | ...          | ...       | ...       |
 | chrX         | 123859390 | 123860728 |
 | chrX         | 1507509   | 1508333   |
 | chrX         | 11362910  | 11363382  |
 | chrX         | 123784707 | 123785245 |
 +--------------+-----------+-----------+
 Unstranded PyRanges object has 10,525 rows and 3 columns from 23 chromosomes.
 For printing, the PyRanges was sorted on Chromosome.}

Best,
xwangda

SeppeDeWinter Aug 30, 2024
Maintainer

HI @xwangda

Can you provide me some info on which function you are running?

Best,

Seppe

xwangda Aug 30, 2024

Hi Seppe,
I was running
regions = markers_dict[DAR].index[markers_dict[DAR].index.str.startswith('chr')] #only keep regions on known chromosomes

I also checked the input data sets of this step:

region_sets

{'topics_otsu': {'Topic1': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 149848826 | 149850326 |
  | chr1         | 28886568  | 28887940  |
  | chr1         | 51235561  | 51237023  |
  | chr1         | 9721673   | 9722016   |
  | ...          | ...       | ...       |
  | chrX         | 150692581 | 150694417 |
  | chrX         | 23662250  | 23662504  |
  | chrX         | 30888592  | 30890016  |
  | chrX         | 131704007 | 131705380 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 5,852 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic2': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 25065414  | 25066295  |
  | chr1         | 184386387 | 184388126 |
  | chr1         | 225460188 | 225461151 |
  | chr1         | 202197489 | 202198231 |
  | ...          | ...       | ...       |
  | chrX         | 10014373  | 10016090  |
  | chrX         | 79161498  | 79162097  |
  | chrX         | 65596144  | 65596608  |
  | chrX         | 19799485  | 19800211  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 5,059 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic3': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 228165185 | 228166754 |
  | chr1         | 30717800  | 30719559  |
  | chr1         | 244862335 | 244864957 |
  | chr1         | 9909257   | 9911251   |
  | ...          | ...       | ...       |
  | chrX         | 130091704 | 130092631 |
  | chrX         | 77894975  | 77895800  |
  | chrX         | 154457534 | 154458979 |
  | chrX         | 15789788  | 15791269  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,022 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic4': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 224182064 | 224183971 |
  | chr1         | 9128144   | 9129842   |
  | chr1         | 40385459  | 40386298  |
  | chr1         | 147598722 | 147600579 |
  | ...          | ...       | ...       |
  | chrX         | 15751195  | 15751838  |
  | chrX         | 65667114  | 65668849  |
  | chrX         | 38560849  | 38561669  |
  | chrX         | 47190536  | 47190981  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 4,096 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic5': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 178605420 | 178606506 |
  | chr1         | 157806420 | 157807208 |
  | chr1         | 38474530  | 38475827  |
  | chr1         | 206050442 | 206051234 |
  | ...          | ...       | ...       |
  | chrX         | 55919348  | 55919758  |
  | chrX         | 17736760  | 17738417  |
  | chrX         | 129769266 | 129769850 |
  | chrX         | 989724    | 990914    |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 5,412 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic6': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 149885351 | 149888651 |
  | chr1         | 1628830   | 1631156   |
  | chr1         | 15975303  | 15976319  |
  | chr1         | 24928581  | 24930714  |
  | ...          | ...       | ...       |
  | chrX         | 154457534 | 154458979 |
  | chrX         | 14872755  | 14873752  |
  | chrX         | 78103464  | 78105113  |
  | chrX         | 44542295  | 44543351  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 4,025 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic7': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 27001566  | 27002447  |
  | chr1         | 19505186  | 19506106  |
  | chr1         | 181134291 | 181135151 |
  | chr1         | 150159537 | 150159821 |
  | ...          | ...       | ...       |
  | chrX         | 109830814 | 109831217 |
  | chrX         | 119605182 | 119606730 |
  | chrX         | 40121046  | 40121624  |
  | chrX         | 96684163  | 96685550  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 9,382 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic8': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 228165185 | 228166754 |
  | chr1         | 30717800  | 30719559  |
  | chr1         | 45685989  | 45687670  |
  | chr1         | 156500293 | 156501591 |
  | ...          | ...       | ...       |
  | chrX         | 16869369  | 16871054  |
  | chrX         | 101931144 | 101932328 |
  | chrX         | 15737297  | 15738981  |
  | chrX         | 47560502  | 47561622  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 2,652 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic9': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 1098739   | 1099904   |
  | chr1         | 183218821 | 183219417 |
  | chr1         | 200530387 | 200531306 |
  | chr1         | 8926676   | 8927741   |
  | ...          | ...       | ...       |
  | chrX         | 102659556 | 102660487 |
  | chrX         | 100636363 | 100636955 |
  | chrX         | 16484086  | 16484672  |
  | chrX         | 136662113 | 136662404 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 6,119 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic10': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 65066468  | 65068123  |
  | chr1         | 150149371 | 150150816 |
  | chr1         | 202348142 | 202349581 |
  | chr1         | 40476775  | 40477889  |
  | ...          | ...       | ...       |
  | chrX         | 18674223  | 18675719  |
  | chrX         | 154804841 | 154805723 |
  | chrX         | 44343323  | 44344998  |
  | chrX         | 54043664  | 54045055  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 4,409 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic11': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 192575275 | 192575897 |
  | chr1         | 159076370 | 159077683 |
  | chr1         | 112957219 | 112957768 |
  | chr1         | 228463559 | 228464986 |
  | ...          | ...       | ...       |
  | chrX         | 48070913  | 48072074  |
  | chrX         | 153947106 | 153947636 |
  | chrX         | 47128875  | 47129885  |
  | chrX         | 110001863 | 110003321 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 7,904 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic12': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 113871377 | 113872612 |
  | chr1         | 248905616 | 248907062 |
  | chr1         | 157137463 | 157139149 |
  | chr1         | 163321100 | 163322302 |
  | ...          | ...       | ...       |
  | chrX         | 131677684 | 131678221 |
  | chrX         | 12901348  | 12901868  |
  | chrX         | 100819543 | 100820693 |
  | chrX         | 41114859  | 41115367  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 5,049 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic13': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 25774542  | 25775769  |
  | chr1         | 206802860 | 206803722 |
  | chr1         | 9728440   | 9729180   |
  | chr1         | 8152361   | 8153664   |
  | ...          | ...       | ...       |
  | chrX         | 108000871 | 108001748 |
  | chrX         | 40589570  | 40590135  |
  | chrX         | 44252892  | 44253849  |
  | chrX         | 330680    | 331636    |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,390 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic14': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 15065640  | 15066495  |
  | chr1         | 167486271 | 167486686 |
  | chr1         | 184386387 | 184388126 |
  | chr1         | 100712509 | 100713549 |
  | ...          | ...       | ...       |
  | chrX         | 44252892  | 44253849  |
  | chrX         | 19343254  | 19344413  |
  | chrX         | 16719000  | 16720167  |
  | chrX         | 65723639  | 65724109  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 5,761 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic15': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 162560744 | 162562405 |
  | chr1         | 226121294 | 226123048 |
  | chr1         | 3624123   | 3625677   |
  | chr1         | 6235267   | 6236382   |
  | ...          | ...       | ...       |
  | chrX         | 37846924  | 37847845  |
  | chrX         | 123962847 | 123963344 |
  | chrX         | 3712239   | 3714008   |
  | chrX         | 48475502  | 48476519  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 4,938 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic16': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 212485869 | 212486259 |
  | chr1         | 31523562  | 31524819  |
  | chr1         | 182149132 | 182149755 |
  | chr1         | 220999969 | 221000919 |
  | ...          | ...       | ...       |
  | chrX         | 154443571 | 154444775 |
  | chrX         | 19814040  | 19814560  |
  | chrX         | 67780446  | 67781089  |
  | chrX         | 110108417 | 110108822 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 7,164 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic17': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 26321003  | 26321828  |
  | chr1         | 25267268  | 25268354  |
  | chr1         | 9653546   | 9654719   |
  | chr1         | 52685853  | 52686581  |
  | ...          | ...       | ...       |
  | chrX         | 129779692 | 129780046 |
  | chrX         | 49922097  | 49923242  |
  | chrX         | 57909343  | 57910852  |
  | chrX         | 119821378 | 119822077 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 6,368 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic18': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 168362775 | 168363478 |
  | chr1         | 53413047  | 53413906  |
  | chr1         | 184840320 | 184840998 |
  | chr1         | 24910762  | 24911702  |
  | ...          | ...       | ...       |
  | chrX         | 85003019  | 85004219  |
  | chrX         | 129769266 | 129769850 |
  | chrX         | 79400326  | 79400907  |
  | chrX         | 129905668 | 129906308 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 5,796 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic19': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 159945312 | 159946071 |
  | chr1         | 26363627  | 26364126  |
  | chr1         | 247330938 | 247332538 |
  | chr1         | 37931135  | 37932180  |
  | ...          | ...       | ...       |
  | chrX         | 21479742  | 21480176  |
  | chrX         | 69158280  | 69158695  |
  | chrX         | 17945154  | 17945407  |
  | chrX         | 153667595 | 153668175 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 7,716 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic20': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 156500293 | 156501591 |
  | chr1         | 10032196  | 10033641  |
  | chr1         | 52636721  | 52637766  |
  | chr1         | 55214330  | 55215866  |
  | ...          | ...       | ...       |
  | chrX         | 21940316  | 21941507  |
  | chrX         | 41332753  | 41335173  |
  | chrX         | 63350539  | 63351581  |
  | chrX         | 120309109 | 120309878 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 4,205 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.},
 'topics_top_3': {'Topic1': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 149848826 | 149850326 |
  | chr1         | 28886568  | 28887940  |
  | chr1         | 51235561  | 51237023  |
  | chr1         | 9721673   | 9722016   |
  | ...          | ...       | ...       |
  | chrX         | 72276504  | 72277510  |
  | chrX         | 103310112 | 103311226 |
  | chrX         | 79336839  | 79337789  |
  | chrX         | 129925388 | 129925975 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic2': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 25065414  | 25066295  |
  | chr1         | 184386387 | 184388126 |
  | chr1         | 225460188 | 225461151 |
  | chr1         | 202197489 | 202198231 |
  | ...          | ...       | ...       |
  | chrX         | 124223500 | 124223919 |
  | chrX         | 48531649  | 48531933  |
  | chrX         | 124342609 | 124343332 |
  | chrX         | 63746129  | 63746649  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic3': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 228165185 | 228166754 |
  | chr1         | 30717800  | 30719559  |
  | chr1         | 244862335 | 244864957 |
  | chr1         | 9909257   | 9911251   |
  | ...          | ...       | ...       |
  | chrX         | 130091704 | 130092631 |
  | chrX         | 77894975  | 77895800  |
  | chrX         | 154457534 | 154458979 |
  | chrX         | 15789788  | 15791269  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic4': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 224182064 | 224183971 |
  | chr1         | 9128144   | 9129842   |
  | chr1         | 40385459  | 40386298  |
  | chr1         | 147598722 | 147600579 |
  | ...          | ...       | ...       |
  | chrX         | 18674223  | 18675719  |
  | chrX         | 15853924  | 15855628  |
  | chrX         | 153609673 | 153611063 |
  | chrX         | 64204790  | 64206508  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic5': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 178605420 | 178606506 |
  | chr1         | 157806420 | 157807208 |
  | chr1         | 38474530  | 38475827  |
  | chr1         | 206050442 | 206051234 |
  | ...          | ...       | ...       |
  | chrX         | 120035813 | 120036368 |
  | chrX         | 13473429  | 13474422  |
  | chrX         | 37818055  | 37818337  |
  | chrX         | 39144972  | 39145304  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic6': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 149885351 | 149888651 |
  | chr1         | 1628830   | 1631156   |
  | chr1         | 15975303  | 15976319  |
  | chr1         | 24928581  | 24930714  |
  | ...          | ...       | ...       |
  | chrX         | 154428213 | 154429056 |
  | chrX         | 48521205  | 48522236  |
  | chrX         | 64394682  | 64395846  |
  | chrX         | 153333586 | 153334704 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic7': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 27001566  | 27002447  |
  | chr1         | 19505186  | 19506106  |
  | chr1         | 181134291 | 181135151 |
  | chr1         | 150159537 | 150159821 |
  | ...          | ...       | ...       |
  | chrX         | 72131287  | 72132300  |
  | chrX         | 68827854  | 68829716  |
  | chrX         | 47619476  | 47620212  |
  | chrX         | 73850786  | 73851873  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic8': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 228165185 | 228166754 |
  | chr1         | 30717800  | 30719559  |
  | chr1         | 45685989  | 45687670  |
  | chr1         | 156500293 | 156501591 |
  | ...          | ...       | ...       |
  | chrX         | 53224003  | 53225712  |
  | chrX         | 147911112 | 147912795 |
  | chrX         | 49155294  | 49156724  |
  | chrX         | 101407112 | 101408743 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic9': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 1098739   | 1099904   |
  | chr1         | 183218821 | 183219417 |
  | chr1         | 200530387 | 200531306 |
  | chr1         | 8926676   | 8927741   |
  | ...          | ...       | ...       |
  | chrX         | 1620744   | 1621403   |
  | chrX         | 30825385  | 30826019  |
  | chrX         | 130091704 | 130092631 |
  | chrX         | 133922936 | 133923477 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic10': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 65066468  | 65068123  |
  | chr1         | 150149371 | 150150816 |
  | chr1         | 202348142 | 202349581 |
  | chr1         | 40476775  | 40477889  |
  | ...          | ...       | ...       |
  | chrX         | 129822986 | 129823443 |
  | chrX         | 136146671 | 136147786 |
  | chrX         | 154443571 | 154444775 |
  | chrX         | 48911126  | 48912374  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic11': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 192575275 | 192575897 |
  | chr1         | 159076370 | 159077683 |
  | chr1         | 112957219 | 112957768 |
  | chr1         | 228463559 | 228464986 |
  | ...          | ...       | ...       |
  | chrX         | 24168976  | 24169514  |
  | chrX         | 47144264  | 47145802  |
  | chrX         | 76427292  | 76428970  |
  | chrX         | 39335755  | 39337249  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic12': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 113871377 | 113872612 |
  | chr1         | 248905616 | 248907062 |
  | chr1         | 157137463 | 157139149 |
  | chr1         | 163321100 | 163322302 |
  | ...          | ...       | ...       |
  | chrX         | 69221952  | 69222408  |
  | chrX         | 18983805  | 18985175  |
  | chrX         | 48675853  | 48677159  |
  | chrX         | 45806018  | 45807160  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic13': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 25774542  | 25775769  |
  | chr1         | 206802860 | 206803722 |
  | chr1         | 9728440   | 9729180   |
  | chr1         | 8152361   | 8153664   |
  | ...          | ...       | ...       |
  | chrX         | 39773881  | 39774590  |
  | chrX         | 106611379 | 106612613 |
  | chrX         | 51892884  | 51893833  |
  | chrX         | 151393529 | 151393840 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic14': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 15065640  | 15066495  |
  | chr1         | 167486271 | 167486686 |
  | chr1         | 184386387 | 184388126 |
  | chr1         | 100712509 | 100713549 |
  | ...          | ...       | ...       |
  | chrX         | 1657207   | 1658212   |
  | chrX         | 46836433  | 46837729  |
  | chrX         | 134718898 | 134719210 |
  | chrX         | 39854484  | 39856039  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic15': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 162560744 | 162562405 |
  | chr1         | 226121294 | 226123048 |
  | chr1         | 3624123   | 3625677   |
  | chr1         | 6235267   | 6236382   |
  | ...          | ...       | ...       |
  | chrX         | 73850786  | 73851873  |
  | chrX         | 154761895 | 154763662 |
  | chrX         | 54529422  | 54530899  |
  | chrX         | 120629488 | 120630494 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic16': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 212485869 | 212486259 |
  | chr1         | 31523562  | 31524819  |
  | chr1         | 182149132 | 182149755 |
  | chr1         | 220999969 | 221000919 |
  | ...          | ...       | ...       |
  | chrX         | 119783064 | 119783375 |
  | chrX         | 1341875   | 1342154   |
  | chrX         | 68666582  | 68666941  |
  | chrX         | 150200991 | 150201301 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 2,995 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic17': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 26321003  | 26321828  |
  | chr1         | 25267268  | 25268354  |
  | chr1         | 9653546   | 9654719   |
  | chr1         | 52685853  | 52686581  |
  | ...          | ...       | ...       |
  | chrX         | 49308626  | 49310030  |
  | chrX         | 68827854  | 68829716  |
  | chrX         | 41275720  | 41276609  |
  | chrX         | 119852428 | 119853378 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic18': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 168362775 | 168363478 |
  | chr1         | 53413047  | 53413906  |
  | chr1         | 184840320 | 184840998 |
  | chr1         | 24910762  | 24911702  |
  | ...          | ...       | ...       |
  | chrX         | 1471620   | 1472166   |
  | chrX         | 124086264 | 124086775 |
  | chrX         | 136629192 | 136629621 |
  | chrX         | 20252428  | 20253296  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic19': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 159945312 | 159946071 |
  | chr1         | 26363627  | 26364126  |
  | chr1         | 247330938 | 247332538 |
  | chr1         | 37931135  | 37932180  |
  | ...          | ...       | ...       |
  | chrX         | 53093636  | 53094619  |
  | chrX         | 85243510  | 85245186  |
  | chrX         | 153983307 | 153983621 |
  | chrX         | 153947106 | 153947636 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Topic20': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 156500293 | 156501591 |
  | chr1         | 10032196  | 10033641  |
  | chr1         | 52636721  | 52637766  |
  | chr1         | 55214330  | 55215866  |
  | ...          | ...       | ...       |
  | chrX         | 71365466  | 71367212  |
  | chrX         | 40644764  | 40645348  |
  | chrX         | 153934341 | 153935473 |
  | chrX         | 63754187  | 63755451  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,000 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.},
 'DARs': {'B': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 178795949 | 178796404 |
  | chr1         | 46332134  | 46332542  |
  | chr1         | 20119205  | 20119762  |
  | chr1         | 174133611 | 174134210 |
  | ...          | ...       | ...       |
  | chrX         | 1239395   | 1240144   |
  | chrX         | 1323248   | 1323578   |
  | chrX         | 51892884  | 51893833  |
  | chrX         | 1554461   | 1555412   |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 8,648 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'CD14Mono': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 162234976 | 162235447 |
  | chr1         | 22745932  | 22746581  |
  | chr1         | 199742575 | 199742899 |
  | chr1         | 112883229 | 112883487 |
  | ...          | ...       | ...       |
  | chrX         | 72100065  | 72101344  |
  | chrX         | 66013200  | 66013739  |
  | chrX         | 41705718  | 41706324  |
  | chrX         | 30652430  | 30653994  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 10,841 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'CD16Mono': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 28714964  | 28715439  |
  | chr1         | 36115919  | 36116228  |
  | chr1         | 87902814  | 87903207  |
  | chr1         | 17141292  | 17142082  |
  | ...          | ...       | ...       |
  | chrX         | 129786333 | 129786670 |
  | chrX         | 12866677  | 12867271  |
  | chrX         | 37754791  | 37755421  |
  | chrX         | 118752026 | 118752718 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 11,297 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'CD3+CD4-CD8-T': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 84876239  | 84876648  |
  | chr1         | 152392855 | 152393315 |
  | chr1         | 147629105 | 147629503 |
  | chr1         | 193458637 | 193459046 |
  | ...          | ...       | ...       |
  | chrX         | 151393529 | 151393840 |
  | chrX         | 12984553  | 12985561  |
  | chrX         | 19566445  | 19566864  |
  | chrX         | 47634744  | 47635190  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 5,386 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'CytotoxicCD8T': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 22633865  | 22634420  |
  | chr1         | 182426790 | 182427072 |
  | chr1         | 168360163 | 168360430 |
  | chr1         | 145716693 | 145717061 |
  | ...          | ...       | ...       |
  | chrX         | 15751195  | 15751838  |
  | chrX         | 136588016 | 136588402 |
  | chrX         | 154541981 | 154543312 |
  | chrX         | 13101578  | 13102097  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 6,081 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'DC': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 28714964  | 28715439  |
  | chr1         | 36115919  | 36116228  |
  | chr1         | 87902814  | 87903207  |
  | chr1         | 64987333  | 64987908  |
  | ...          | ...       | ...       |
  | chrX         | 154056716 | 154057176 |
  | chrX         | 16484086  | 16484672  |
  | chrX         | 15493122  | 15493705  |
  | chrX         | 10198906  | 10199633  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 11,125 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'NK': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 84371000  | 84371340  |
  | chr1         | 157399861 | 157400388 |
  | chr1         | 1221863   | 1222184   |
  | chr1         | 162411603 | 162412344 |
  | ...          | ...       | ...       |
  | chrX         | 13486955  | 13487226  |
  | chrX         | 12984553  | 12985561  |
  | chrX         | 1462646   | 1463302   |
  | chrX         | 44012566  | 44013076  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 6,110 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'NaiveCD4T': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 59892761  | 59893688  |
  | chr1         | 213711925 | 213712434 |
  | chr1         | 24475663  | 24475981  |
  | chr1         | 183033207 | 183033531 |
  | ...          | ...       | ...       |
  | chrX         | 154056716 | 154057176 |
  | chrX         | 150410142 | 150410881 |
  | chrX         | 135383975 | 135384563 |
  | chrX         | 16484086  | 16484672  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 4,374 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'NaiveCD8T': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 24475663  | 24475981  |
  | chr1         | 59892761  | 59893688  |
  | chr1         | 88661195  | 88661602  |
  | chr1         | 213711925 | 213712434 |
  | ...          | ...       | ...       |
  | chrX         | 73977303  | 73977964  |
  | chrX         | 136694162 | 136695069 |
  | chrX         | 41382866  | 41384365  |
  | chrX         | 13151575  | 13152295  |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 3,602 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.,
  'Neutrophil': +--------------+-----------+-----------+
  | Chromosome   | Start     | End       |
  | (category)   | (int32)   | (int32)   |
  |--------------+-----------+-----------|
  | chr1         | 19436687  | 19436992  |
  | chr1         | 161506474 | 161507008 |
  | chr1         | 246608899 | 246609314 |
  | chr1         | 179175307 | 179175917 |
  | ...          | ...       | ...       |
  | chrX         | 1336074   | 1337137   |
  | chrX         | 110089672 | 110090276 |
  | chrX         | 1517248   | 1517703   |
  | chrX         | 136768517 | 136768795 |
  +--------------+-----------+-----------+
  Unstranded PyRanges object has 7,116 rows and 3 columns from 23 chromosomes.
  For printing, the PyRanges was sorted on Chromosome.}}

#markers_dict
{'B':                             Log2FC  Adjusted_pval Contrast
 chr3:167829080-167829630  4.717465   0.000000e+00        B
 chr5:89342033-89342451    4.717465   0.000000e+00        B
 chr7:108294666-108294916  4.717465   0.000000e+00        B
 chr18:55997101-55997583   4.717465   0.000000e+00        B
 chr3:19559723-19560162    4.713637   0.000000e+00        B
 ...                            ...            ...      ...
 chr6:70412752-70414397    0.587107   0.000000e+00        B
 chr6:135306784-135307298  0.587064  1.635038e-193        B
 chr3:53218185-53218398    0.586595  3.759230e-183        B
 chr22:40385126-40385985   0.586089  7.058049e-139        B
 chr17:30953071-30953281   0.585950  1.171009e-199        B
 
 [8648 rows x 3 columns],
 'CD14Mono':                             Log2FC  Adjusted_pval  Contrast
 chr4:111991791-111992075  4.931932  2.357017e-285  CD14Mono
 chr5:60232153-60232745    4.931932  2.357017e-285  CD14Mono
 chr18:10290245-10290620   4.931932  2.357017e-285  CD14Mono
 chr19:44868888-44869181   4.931932  2.357017e-285  CD14Mono
 chr21:32371793-32372155   4.931932  2.357017e-285  CD14Mono
 ...                            ...            ...       ...
 chr16:56911665-56912213   0.586860   2.491780e-53  CD14Mono
 chr17:4738467-4740130     0.586688  1.247988e-162  CD14Mono
 chr1:182962541-182962831  0.585941   3.648514e-57  CD14Mono
 chr2:37934335-37934897    0.585842   1.697430e-50  CD14Mono
 chr7:5229580-5229988      0.585302   1.128723e-40  CD14Mono
 
 [10841 rows x 3 columns],
 'CD16Mono':                              Log2FC  Adjusted_pval  Contrast
 chr10:113321001-113321310  4.038295   2.821443e-66  CD16Mono
 chr15:32866590-32867176    4.025242   2.821443e-66  CD16Mono
 chr17:68491371-68491686    4.021741   2.821443e-66  CD16Mono
 chr6:146357636-146358188   4.020743   2.821443e-66  CD16Mono
 chr2:121287257-121287697   4.018307   2.821443e-66  CD16Mono
 ...                             ...            ...       ...
 chr19:54338689-54339294    0.586818   1.881137e-15  CD16Mono
 chr5:172833627-172834966   0.586387   1.172684e-36  CD16Mono
 chr15:64044423-64044877    0.585250   7.472606e-16  CD16Mono
 chr18:55321484-55322767    0.585217   2.223547e-13  CD16Mono
 chr22:22343432-22343874    0.585133   4.216898e-10  CD16Mono
 
 [11297 rows x 3 columns],
 'CD3+CD4-CD8-T':                             Log2FC  Adjusted_pval       Contrast
 chr13:41974383-41974841   2.433025   5.051866e-46  CD3+CD4-CD8-T
 chr22:31958615-31958999   2.419592   4.766950e-46  CD3+CD4-CD8-T
 chr1:84876239-84876648    2.413770   5.051866e-46  CD3+CD4-CD8-T
 chr3:33030811-33031109    2.408908   7.069289e-46  CD3+CD4-CD8-T
 chr17:1707180-1707384     2.408760   4.766950e-46  CD3+CD4-CD8-T
 ...                            ...            ...            ...
 chr6:89475567-89475962    0.585612   4.352479e-18  CD3+CD4-CD8-T
 chr4:82992483-82993096    0.585577   1.098878e-16  CD3+CD4-CD8-T
 chr17:28371025-28372544   0.585197   1.692318e-34  CD3+CD4-CD8-T
 chr10:3805121-3805587     0.585094   2.579044e-26  CD3+CD4-CD8-T
 chr5:157025098-157025702  0.585027   2.580666e-15  CD3+CD4-CD8-T
 
 [5386 rows x 3 columns],
 'CytotoxicCD8T':                             Log2FC  Adjusted_pval       Contrast
 chr7:29255941-29256336    2.967617  1.218105e-288  CytotoxicCD8T
 chr16:82432187-82432600   2.958885  3.059075e-288  CytotoxicCD8T
 chr6:127924514-127924736  2.953621  3.200544e-289  CytotoxicCD8T
 chr2:12948228-12948878    2.946508  8.277879e-293  CytotoxicCD8T
 chrX:109794040-109794649  2.945389  1.931535e-288  CytotoxicCD8T
 ...                            ...            ...            ...
 chr10:7318022-7318378     0.585527   1.322697e-45  CytotoxicCD8T
 chr1:93758552-93759336    0.585455  6.399498e-151  CytotoxicCD8T
 chr16:88633563-88635068   0.585375  3.409524e-149  CytotoxicCD8T
 chr6:139291618-139292272  0.585271  3.787333e-141  CytotoxicCD8T
 chrX:13101578-13102097    0.585263  3.636046e-118  CytotoxicCD8T
 
 [6081 rows x 3 columns],
 'DC':                              Log2FC  Adjusted_pval Contrast
 chr10:113321001-113321310  3.486217   1.255054e-21       DC
 chr15:32866590-32867176    3.483390   1.255054e-21       DC
 chr7:56000084-56000444     3.481256   1.255054e-21       DC
 chr17:68491371-68491686    3.479729   1.255054e-21       DC
 chr6:146357636-146358188   3.475265   1.255054e-21       DC
 ...                             ...            ...      ...
 chr11:64355127-64355332    0.586005   1.455474e-05       DC
 chr9:5536520-5537033       0.585842   3.093816e-04       DC
 chr1:52641271-52641549     0.585471   1.558251e-06       DC
 chr1:56472724-56473213     0.585271   3.153830e-04       DC
 chr9:27377401-27378460     0.585137   9.705626e-07       DC
 
 [11125 rows x 3 columns],
 'NK':                              Log2FC  Adjusted_pval Contrast
 chr12:100303579-100304183  4.308378  5.634524e-220       NK
 chr20:25982602-25982978    4.291842  5.839160e-220       NK
 chr1:84371000-84371340     4.280005  4.650434e-220       NK
 chr14:84036864-84037243    4.276156  2.349988e-220       NK
 chr4:7435330-7435654       4.268943  8.148634e-220       NK
 ...                             ...            ...      ...
 chr17:75864294-75865233    0.585599   9.883310e-70       NK
 chr4:89303165-89303470     0.585457   1.293798e-50       NK
 chr7:157299526-157300295   0.585189   3.449320e-44       NK
 chr1:181061964-181063099   0.585116   4.248139e-78       NK
 chr17:82230678-82231349    0.584979  2.806759e-114       NK
 
 [6110 rows x 3 columns],
 'NaiveCD4T':                              Log2FC  Adjusted_pval   Contrast
 chr2:172943401-172943891   2.293163   0.000000e+00  NaiveCD4T
 chrX:154693393-154693681   2.281430   0.000000e+00  NaiveCD4T
 chr4:22444205-22444738     2.279597   0.000000e+00  NaiveCD4T
 chr6:121959446-121959769   2.278924   0.000000e+00  NaiveCD4T
 chr12:122326379-122326890  2.276551   0.000000e+00  NaiveCD4T
 ...                             ...            ...        ...
 chr20:63101560-63103259    0.586921  8.529551e-221  NaiveCD4T
 chr2:98448201-98448852     0.586882   6.618174e-78  NaiveCD4T
 chr2:239225352-239225722   0.585616  9.451764e-123  NaiveCD4T
 chr15:52481699-52482365    0.585391  2.165712e-227  NaiveCD4T
 chr5:139565315-139565826   0.585220  7.253390e-228  NaiveCD4T
 
 [4374 rows x 3 columns],
 'NaiveCD8T':                              Log2FC  Adjusted_pval   Contrast
 chr11:33021711-33022261    1.734293   3.371096e-41  NaiveCD8T
 chr10:6595473-6595701      1.733395   1.595831e-40  NaiveCD8T
 chr2:109102676-109103282   1.714876   2.755454e-42  NaiveCD8T
 chrX:154693393-154693681   1.708979   5.449223e-40  NaiveCD8T
 chr2:172943401-172943891   1.705553   2.371044e-39  NaiveCD8T
 ...                             ...            ...        ...
 chr14:74922605-74923488    0.586042   4.925718e-30  NaiveCD8T
 chr12:132904547-132905066  0.585797   1.021963e-29  NaiveCD8T
 chr8:120730886-120732532   0.585520   2.331589e-22  NaiveCD8T
 chr21:42527266-42528105    0.585490   3.884522e-14  NaiveCD8T
 chr19:49567767-49568545    0.585308   6.665616e-12  NaiveCD8T
 
 [3602 rows x 3 columns],
 'Neutrophil':                             Log2FC  Adjusted_pval    Contrast
 chr12:32589177-32589786   1.402214   5.439229e-09  Neutrophil
 chr7:17009117-17009708    1.392601   4.172238e-09  Neutrophil
 chr10:97408569-97408771   1.391406   4.172238e-09  Neutrophil
 chr17:75228277-75228649   1.388752   4.172238e-09  Neutrophil
 chr12:6092945-6093713     1.383264   4.172238e-09  Neutrophil
 ...                            ...            ...         ...
 chr13:99124735-99125253   0.585474   1.599783e-03  Neutrophil
 chr3:46892267-46892794    0.585406   4.638273e-08  Neutrophil
 chr3:46097488-46098762    0.585299   1.995390e-07  Neutrophil
 chr8:6291319-6292188      0.585267   3.292087e-04  Neutrophil
 chr2:240998200-240998901  0.585055   1.642869e-06  Neutrophil
 
 [7116 rows x 3 columns],
 'Platelet': Empty DataFrame
 Columns: [Log2FC, Adjusted_pval, Contrast]
 Index: [],
 'RegulatoryCD4T':                             Log2FC  Adjusted_pval        Contrast
 chr2:204027044-204027404  1.701831  2.507813e-140  RegulatoryCD4T
 chr4:152606856-152607323  1.689903  8.373597e-143  RegulatoryCD4T
 chr12:76456888-76457322   1.680787  1.707321e-159  RegulatoryCD4T
 chr2:96359892-96360157    1.673000  5.945933e-133  RegulatoryCD4T
 chr6:11785912-11786407    1.654258  1.026593e-165  RegulatoryCD4T
 ...                            ...            ...             ...
 chr11:14569372-14569910   0.585645   2.102041e-71  RegulatoryCD4T
 chr2:236967816-236968405  0.585357   1.710733e-55  RegulatoryCD4T
 chr16:57134466-57135308   0.585290  2.990003e-113  RegulatoryCD4T
 chr6:5173859-5175092      0.585240  3.224091e-100  RegulatoryCD4T
 chr2:160651955-160652661  0.585151   2.592632e-74  RegulatoryCD4T
 
 [3232 rows x 3 columns]}

I think the files look OK and I have no idea why I have this error:
ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements.

Any suggestions or advice would be really helpful, thank you so much!

Best,
xwangda

SeppeDeWinter Sep 3, 2024
Maintainer

Hi @xwangda

The command you were running should not produce this error..
This is the exact code you ran before you got the error?

All the best,

Seppe

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Length mismatch: Expected axis has 0 elements, new values have 3 elements #286

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Length mismatch: Expected axis has 0 elements, new values have 3 elements #286

Sudheshna30 Jan 17, 2024

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