yojetsharma
commented
1 week ago Describe the bug I am running pycisTopic and everything ran smoothly until i reached the step of creating a merged cis_obj_list:
import warnings warnings.simplefilter(action='ignore') import pandas import pycisTopic pycisTopic.__version__ '2.0a0' path_to_regions = os.path.join(out_dir, "consensus_peak_calling/consensus_regions.bed") path_to_blacklist = "/home/praghu/yojetsharma/softwares/pycisTopic/blacklist/hg38-blacklist.v2.bed" pycistopic_qc_output_dir = "qc" from pycisTopic.cistopic_class import create_cistopic_object_from_fragments import polars as pl cistopic_obj_list = [] for sample_id in fragments_dict: sample_metrics = pl.read_parquet( os.path.join(pycistopic_qc_output_dir, f'{sample_id}.fragments_stats_per_cb.parquet') ).to_pandas().set_index("CB").loc[ sample_id_to_barcodes_passing_filters[sample_id] ] cistopic_obj = create_cistopic_object_from_fragments( path_to_fragments = fragments_dict[sample_id], path_to_regions = path_to_regions, path_to_blacklist = path_to_blacklist, metrics = sample_metrics, valid_bc = sample_id_to_barcodes_passing_filters[sample_id], n_cpu = 1, project = sample_id, split_pattern = '-' ) cistopic_obj_list.append(cistopic_obj) 2024-09-15 12:15:30,495 cisTopic INFO Reading data for d149 2024-09-15 12:18:25,421 cisTopic INFO metrics provided! 2024-09-15 12:18:39,466 cisTopic INFO Counting fragments in regions 2024-09-15 12:20:54,984 cisTopic INFO Creating fragment matrix /ncbs_gs/nlsas_data/usershares/praghu/yojetsharma/softwares/pycisTopic/src/pycisTopic/cistopic_class.py:886: PerformanceWarning: The following operation may generate 6280216839 cells in the resulting pandas object. .unstack(level="Name", fill_value=0) 2024-09-15 12:23:19,172 cisTopic INFO Converting fragment matrix to sparse matrix 2024-09-15 12:24:09,916 cisTopic INFO Removing blacklisted regions 2024-09-15 12:24:11,687 cisTopic INFO Creating CistopicObject 2024-09-15 12:24:15,938 cisTopic INFO Done! 2024-09-15 12:24:17,884 cisTopic INFO Reading data for ls002 2024-09-15 12:27:16,855 cisTopic INFO metrics provided! 2024-09-15 12:27:30,732 cisTopic INFO Counting fragments in regions 2024-09-15 12:29:53,260 cisTopic INFO Creating fragment matrix /ncbs_gs/nlsas_data/usershares/praghu/yojetsharma/softwares/pycisTopic/src/pycisTopic/cistopic_class.py:886: PerformanceWarning: The following operation may generate 11394507046 cells in the resulting pandas object. .unstack(level="Name", fill_value=0) 2024-09-15 12:33:34,320 cisTopic INFO Converting fragment matrix to sparse matrix 2024-09-15 12:35:22,478 cisTopic INFO Removing blacklisted regions 2024-09-15 12:35:24,316 cisTopic INFO Creating CistopicObject 2024-09-15 12:35:29,299 cisTopic INFO Done! 2024-09-15 12:35:31,288 cisTopic INFO Reading data for ls003 2024-09-15 12:39:03,988 cisTopic INFO metrics provided! 2024-09-15 12:39:20,066 cisTopic INFO Counting fragments in regions 2024-09-15 12:42:09,488 cisTopic INFO Creating fragment matrix /ncbs_gs/nlsas_data/usershares/praghu/yojetsharma/softwares/pycisTopic/src/pycisTopic/cistopic_class.py:886: PerformanceWarning: The following operation may generate 7762093599 cells in the resulting pandas object. .unstack(level="Name", fill_value=0) 2024-09-15 12:49:48,158 cisTopic INFO Converting fragment matrix to sparse matrix 2024-09-15 12:50:58,834 cisTopic INFO Removing blacklisted regions 2024-09-15 12:51:02,252 cisTopic INFO Creating CistopicObject 2024-09-15 12:51:11,716 cisTopic INFO Done! cistopic_obj = merge(cistopic_obj_list) --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[27], line 1 ----> 1 cistopic_obj = merge(cistopic_obj_list) NameError: name 'merge' is not definedTo Reproduce Commands relevant to reproduce the error.
Error output Paste the entire output of the command, including log information prior to the error.
Expected behavior I would expect it the merge() function to run as is described in the notebook:
cistopic_obj = merge(cistopic_obj_list) 2022-08-09 09:58:30,928 cisTopic INFO cisTopic object 1 merged 2022-08-09 09:58:41,004 cisTopic INFO cisTopic object 2 merged 2022-08-09 09:58:53,013 cisTopic INFO cisTopic object 3 merged 2022-08-09 09:59:09,175 cisTopic INFO cisTopic object 4 merged In [8]:Screenshots If applicable, add screenshots to help explain your problem or show the format of the input data for the command/s.
Version (please complete the following information):
- Python.3.11
Additional context Add any other context about the problem here.
Okay, I was able to solve this by first calling the CistopicObject and then merge. dir(pycisTopic) gave me:
['DistributionNotFound',
'__builtins__',
'__cached__',
'__doc__',
'__file__',
'__loader__',
'__name__',
'__package__',
'__path__',
'__spec__',
'__version__',
'__warningregistry__',
'cistopic_class',
'contextlib',
'fragments',
'genomic_ranges',
'get_distribution',
'plotting',
'qc',
'topic_binarization',
'tss_profile',
'utils']
import pycisTopic.cistopic_class as cistopic_classFigured merge would be in cistopic_class so listed that:
# List all attributes and methods in the module
print(dir(cistopic_class))
# Check for the class directly
print(hasattr(cistopic_class, 'CistopicObject'))
['CistopicObject', 'Self', 'TYPE_CHECKING', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__spec__', '__warningregistry__', 'annotations', 'cl', 'collapse_duplicates', 'create_cistopic_object', 'create_cistopic_object_chunk', 'create_cistopic_object_from_fragments', 'create_cistopic_object_from_matrix_file', 'dtype', 'get_position_index', 'logging', 'merge', 'non_zero_rows', 'np', 'pd', 'pr', 'prepare_tag_cells', 'read_fragments_to_pyranges', 'region_names_to_coordinates', 'sp', 'sparse', 'subset_list', 'sys']
TrueFound merge here and so imported that:
**from pycisTopic.cistopic_class import CistopicObject, merge**
cistopic_obj = merge(cistopic_obj_list)
2024-09-15 13:31:30,536 cisTopic INFO cisTopic object 1 merged
2024-09-15 13:31:49,202 cisTopic INFO cisTopic object 2 merged
print(cistopic_obj)
CistopicObject from project cisTopic_merge with n_cells × n_regions = 60499 × 420461But still don't understand why it wouldn't import the function?
Describe the bug I am running pycisTopic and everything ran smoothly until i reached the step of creating a merged cis_obj_list:
To Reproduce Commands relevant to reproduce the error.
Error output Paste the entire output of the command, including log information prior to the error.
Expected behavior I would expect it the merge() function to run as is described in the notebook:
Screenshots If applicable, add screenshots to help explain your problem or show the format of the input data for the command/s.
Version (please complete the following information):
Additional context Add any other context about the problem here.