[BUG] TypeError: Must supply at least one delayed object

[Achiraa]

TypeError: Must supply at least one delayed object

Input matrix

ex_matrix = pd.read_csv(SC_EXP_FNAME, sep='\t', header=0, index_col=0).T
ex_matrix.head()
GENE Mrpl15 Lypla1 Gm37988 Tcea1 Atp6v1h Rb1cc1 4732440D04Rik Pcmtd1 Gm26901 Rrs1 Adhfe1 Mybl1
BM_AAACCCAAGTCTAGAA.1 0.000000 1.098612 0.0 0.000000 0.000000 0.693147 0.000000 0.693147 0.0 0.693147 0.0 0.0

Code
1. Command run when the error occurred:
import os
import glob
import pickle
import pyscenic
import pandas as pd
import numpy as np
import seaborn as sns
import dask.dataframe as dd

from dask.diagnostics import ProgressBar

from arboreto.utils import load_tf_names
from arboreto.algo import grnboost2

from ctxcore.rnkdb import FeatherRankingDatabase as RankingDatabase
from pyscenic.utils import modules_from_adjacencies, load_motifs
from pyscenic.prune import prune2df, df2regulons
from pyscenic.aucell import aucell

DATA_FOLDER="C:/Users/S236282/Desktop/Itaconate data/pySCENIC"
RESOURCES_FOLDER="C:/Users/S236282/Desktop/Itaconate data/pySCENIC"
DATABASE_FOLDER = "C:/Users/S236282/Desktop/Itaconate data/pySCENIC"

DATABASES_GLOB = os.path.join(DATA_FOLDER, "mm10_*.genes_vs_motifs.rankings.feather")
MOTIF_ANNOTATIONS_FNAME = os.path.join(RESOURCES_FOLDER, "motifs-v10nr_clustnr_mgi.tbl")

MM_TFS_FNAME = os.path.join(RESOURCES_FOLDER, 'allTFs_mm.txt')
SC_EXP_FNAME = os.path.join(RESOURCES_FOLDER, "Expression_data.txt")

ADJACENCIES_FNAME = os.path.join(RESOURCES_FOLDER, "adjacencies.tsv")
MODULES_FNAME = os.path.join(RESOURCES_FOLDER, "modules.p")
MOTIFS_FNAME = os.path.join(RESOURCES_FOLDER, "motifs.csv")
REGULONS_FNAME = os.path.join(RESOURCES_FOLDER, "regulons.p")

N_SAMPLES = 500

ex_matrix = pd.read_csv(SC_EXP_FNAME, sep='\t', header=0, index_col=0).T
ex_matrix.head()
ex_matrix.shape

tf_name = load_tf_names(MM_TFS_FNAME)

db_fnames = glob.glob(DATABASES_GLOB)

def name(fname):
return os.path.splitext(os.path.basename(fname))[0]

dbs = [RankingDatabase(fname=fname, name=name(fname)) for fname in db_fnames]
dbs

filtered_tf_name = list(intersection)

adjacencies = grnboost2(expression_data=ex_matrix, tf_names= tf_name, verbose=True)
adjancencies.head()

2. Error encountered:

adjacencies = grnboost2(expression_data=ex_matrix, tf_names= tf_name, verbose=True)
preparing dask client
parsing input
creating dask graph
shutting down client and local cluster
finished
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\arboreto\algo.py", line 39, in grnboost2
return diy(expression_data=expression_data, regressor_type='GBM', regressor_kwargs=SGBM_KWARGS,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\arboreto\algo.py", line 120, in diy
graph = create_graph(expression_matrix,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\arboreto\core.py", line 450, in create_graph
all_meta_df = from_delayed(delayed_meta_dfs, meta=_META_SCHEMA)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\dask_expr\io_delayed.py", line 115, in from_delayed
raise TypeError("Must supply at least one delayed object")
TypeError: Must supply at least one delayed object

Expected behavior
A clear and concise description of what you expected to happen.

Please complete the following information:

• pySCENIC version: 0.12.1
• Installation method: Pip
• Run environment: Python 3.11.9
• OS: Windows
• Package versions:
• aiohappyeyeballs==2.4.3
  aiohttp==3.10.10
  aiosignal==1.3.1
  arboreto==0.1.6
  attrs==24.2.0
  bokeh==3.6.0
  boltons==24.0.0
  certifi==2024.8.30
  charset-normalizer==3.4.0
  click==8.1.7
  cloudpickle==3.1.0
  colorama==0.4.6
  contourpy==1.3.0
  ctxcore==0.2.0
  cycler==0.12.1
  cytoolz==1.0.0
  dask==2024.10.0
  dask-expr==1.1.16
  dill==0.3.9
  distributed==2024.2.1
  fonttools==4.54.1
  frozendict==2.4.6
  frozenlist==1.5.0
  fsspec==2024.10.0
  h5py==3.12.1
  idna==3.10
  importlib_metadata==8.5.0
  interlap==0.2.7
  Jinja2==3.1.4
  joblib==1.4.2
  kiwisolver==1.4.7
  llvmlite==0.43.0
  locket==1.0.0
  loompy==3.0.7
  lz4==4.3.3
  MarkupSafe==3.0.2
  matplotlib==3.9.2
  msgpack==1.1.0
  multidict==6.1.0
  multiprocessing_on_dill==3.5.0a4
  networkx==3.4.2
  numba==0.60.0
  numexpr==2.10.1
  numpy==2.0.2
  numpy-groupies==0.11.2
  packaging==24.1
  pandas==2.2.3
  partd==1.4.2
  pillow==11.0.0
  propcache==0.2.0
  psutil==6.1.0
  pyarrow==18.0.0
  pynndescent==0.5.13
  pyparsing==3.2.0
  pyscenic==0.12.1
  python-dateutil==2.9.0.post0
  pytz==2024.2
  PyYAML==6.0.2
  requests==2.32.3
  scikit-learn==1.5.2
  scipy==1.14.1
  seaborn==0.13.2
  six==1.16.0
  sortedcontainers==2.4.0
  tblib==3.0.0
  threadpoolctl==3.5.0
  toolz==1.0.0
  tornado==6.4.1
  tqdm==4.66.6
  tzdata==2024.2
  umap-learn==0.5.7
  urllib3==2.2.3
  xyzservices==2024.9.0
  yarl==1.17.1
  zict==3.0.0
  zipp==3.20.2

[meriadecmorrier]

Hi,
It looks like issue #561. It might be linked to your dask-expr version (1.1.16) ?
Best

[Achiraa]

Thank you. Unfortunately, it didn't work for me. it raised another error.

TypeError: descriptor 'call' for 'type' objects doesn't apply to a 'property' object

[olaf-c]

I'm having the same bug, did you find a solution?

[Achiraa]

Hi, I was not able to resolve this issue, but I tried using docker approach. It works and is easy. Here is the link: https://pyscenic.readthedocs.io/en/latest/installation.html

[ruoyeruolan]

This issue is caused by the create_graph function in arboreto.core. To resolve it, simply comment out the second command. While this error has already been fixed on GitHub, it has not yet been addressed in version 0.1.6 of the package.