Module 'cptac' has no attribute 'INDEX'

[mavershang]

A1BG_cross = ov.multi_join({"umich proteomics": "A1BG", "bcm transcriptomics": "A1BG"})

Trace
AttributeError Traceback (most recent call last)
Cell In[17], line 1
----> 1 A1BG_cross = ov.multi_join({"umich proteomics": "A1BG", "bcm transcriptomics": "A1BG"})

File c:\Users\shang\Documents\cptac\venv\Lib\site-packages\cptac\cancers\cancer.py:525, in Cancer.multi_join(self, join_dict, mutations_filter, flatten, levels_to_drop, how, tissue_type)
521 raise DataFrameNotIncludedError(
522 f"{source} {datatype} is not a valid dataframe in the {self.get_cancer_type()} dataset.")
524 # Get the relevant columns
--> 525 columns = self._get_columns(datatype, source, data_key, tissue_type, mutations_filter)
527 # Set flag that mutations data in join_dict
528 if datatype == "somatic_mutation":

File c:\Users\shang\Documents\cptac\venv\Lib\site-packages\cptac\cancers\cancer.py:467, in Cancer._get_columns(self, datatype, source, data_key, tissue_type, mutations_filter)
465 columns = self._get_omics_cols(datatype, source, found_genes or None, tissue_type=tissue_type)
466 else:
--> 467 columns = self._get_omics_cols(datatype, source, data_key or None, tissue_type=tissue_type)
468 # If key belongs to metadata
469 elif datatype in self._valid_metadata_dfs:

File c:\Users\shang\Documents\cptac\venv\Lib\site-packages\cptac\cancers\cancer.py:778, in Cancer._get_omics_cols(self, omics_df_name, source, genes, tissue_type)
775 self._check_df_valid(omics_df_name, source, "omics")
777 # Get our omics df, using get_dataframe to catch invalid requests
--> 778 omics_df = self.get_dataframe(omics_df_name, source, tissue_type).copy()
780 # Process genes parameter
...
--> 126 if local_hash != cptac.INDEX.loc[cptac.INDEX['filename']==prefixed_file, 'checksum'].item():
127 warn(FailedChecksumWarning("Local file and online file have different checksums; redownloading data"))
128 os.remove(file_path)

AttributeError: module 'cptac' has no attribute 'INDEX'

[bm600]

Hey sorry for the delay. I've run the same code on my machine and on google colab and it seems to work as intended. Do you have any more details that could be helpful? Are you sure you're on the latest version? This is the code that I've run that works on my machine:

import cptac

ov = cptac.Ov()
A1BG_cross = ov.multi_join({"umich proteomics": "A1BG", "bcm transcriptomics": "A1BG"})
A1BG_cross.head()

Let me know if there's anything I can do to help! Thanks!

[sooheon]

I am getting the same error. cptac.version() is 1.5.14, python is 3.12.4

[sooheon]

Seems like a python issue -- rerunning with python 3.10 avoids this error