Error in cancer.py file

[janamace]

Hello,

After installing the cptac package I am having this problem. can you help me?

import cptac

TypeError Traceback (most recent call last)
in
----> 1 import cptac

~\anaconda3\lib\site-packages\cptac_init_.py in
30
31 # Dataset imports
---> 32 from cptac.cancers.brca import Brca
33 from cptac.cancers.ccrcc import Ccrcc
34 from cptac.cancers.coad import Coad

~\anaconda3\lib\site-packages\cptac\cancers\brca.py in
10 # limitations under the License.
11
---> 12 from cptac.cancers.cancer import Cancer
13
14 # Import various BRCA data sources

~\anaconda3\lib\site-packages\cptac\cancers\cancer.py in
23 from cptac.tools.dataframe_tools import add_index_levels, join_col_to_dataframe
24
---> 25 class Cancer:
26 NORMAL_ENDINGS = ('.N', '.C') # HNSCC data has cored normal samples marked .C
27 """Note that all cancer datasets are class objects that inherit

~\anaconda3\lib\site-packages\cptac\cancers\cancer.py in Cancer()
1000 return df
1001
-> 1002 def _format_mutations_data(self, mutations: pd.DataFrame, mutations_were_filtered: bool, show_location: bool=True, how: str="outer", quiet: bool=False, tissue_type: str="both", mutation_cols: list[str] or str=["Mutation","Location"]
1003 ) -> pd.DataFrame:
1004 """Format mutations data. Add a Sample_Status column, fill in NaNs with Wildtype_Normal or Wildtype_Tumor.

TypeError: 'type' object is not subscriptable

[sabmel]

I'm so sorry about the inconvenience. Would you mind letting us know what version of cptac you are currently running?

[janamace]

Hi Sabrina,

Thank you for your answer! I'm using these versions of cptac, pandas, and, pip, conda, and numexpr:

numexpr 2.7.3
cptac 1.5.1
conda 4.14.0
pandas 2.0.3
pip 23.2.1

[sabmel]

Thank you! I'm not entirely sure why it's throwing that error for you, but we just released a new update, so go ahead and update and see if the issue persists. I appreciate your patience!

…

On Thu, Sep 28, 2023 at 12:41 AM janamace ***@***.***> wrote: Hi Sabrina, Thank you for your answer! I'm using these versions of cptac, pandas, and, pip, conda, and numexpr: numexpr 2.7.3 cptac 1.5.1 conda 4.14.0 pandas 2.0.3 pip 23.2.1 — Reply to this email directly, view it on GitHub <#45 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGAFPT42SPZUBP3OAMIQMWTX4ULZXANCNFSM6AAAAAA5HU3MY4> . You are receiving this because you commented.Message ID: ***@***.***>

[lincoln-harris]

Excited to use this package, but I'm getting the same issue when trying to import cptac v1.5.7. Specifically:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[1], line 1
----> 1 import cptac

File ~/miniconda3/envs/cptac/lib/python3.8/site-packages/cptac/__init__.py:32
     29 from cptac.utils.other_utils import df_to_tree
     31 # Dataset imports
---> 32 from cptac.cancers.brca import Brca
     33 from cptac.cancers.ccrcc import Ccrcc
     34 from cptac.cancers.coad import Coad

File ~/miniconda3/envs/cptac/lib/python3.8/site-packages/cptac/cancers/brca.py:12
      1 #   Copyright 2023 Samuel Payne sam_payne@byu.edu
      2 #   Licensed under the Apache License, Version 2.0 (the "License");
      3 #   you may not use this file except in compliance with the License.
   (...)
      9 #   See the License for the specific language governing permissions and
     10 #   limitations under the License.
---> 12 from cptac.cancers.cancer import Cancer
     14 # Import various BRCA data sources
     15 from cptac.cancers.bcm.bcmbrca import BcmBrca

File ~/miniconda3/envs/cptac/lib/python3.8/site-packages/cptac/cancers/cancer.py:25
     22 from cptac.exceptions import *
     23 from cptac.tools.dataframe_tools import add_index_levels, join_col_to_dataframe
---> 25 class Cancer:
     26     NORMAL_ENDINGS = ('.N', '.C') # HNSCC data has cored normal samples marked .C
     27     """Note that all cancer datasets are class objects that inherit 
     28         from cptac.cancer.
     29     Therefore the same function calls exist for cptac.Brca, cptac.Gbm, etc.
     30     """

File ~/miniconda3/envs/cptac/lib/python3.8/site-packages/cptac/cancers/cancer.py:1002, in Cancer()
    998         df.columns.name = "Name"
   1000     return df
-> 1002 def _format_mutations_data(self, mutations: pd.DataFrame, mutations_were_filtered: bool, show_location: bool=True, how: str="outer", quiet: bool=False, tissue_type: str="both", mutation_cols: list[str] or str=["Mutation","Location"]
   1003                            ) -> pd.DataFrame:
   1004     """Format mutations data. Add a Sample_Status column, fill in NaNs with Wildtype_Normal or Wildtype_Tumor.
   1005     Note: This is mostly so that the multi_join function can behave the same way as the old join functions.
   1006     join_other_to_mutations does this same formatting, and should probably be refactored to use this.
   (...)
   1017     pandas.DataFrame: The joined dataframe, with a Sample_Status column added and NaNs filled.
   1018     """
   1020     # Add Sample_Status column

TypeError: 'type' object is not subscriptable