jinmiaochenlab/discotoolkit_py

Python version of DISCO toolkit

discotoolkit_py's Issues

an error is reported when getting metadata

Hi,

Thank you for your amazing tool!

When I used discotoolkit to get the sample's matadata, I found an error.

my code

import discotoolkit as dt

filter = dt.Filter(
    platform=["10x3'", "10x5'"]
)
metadata = dt.filter_disco_metadata(filter)
print(metadata.sample_metadata.shape)

the error

INFO:root:Retrieving metadata from DISCO database
INFO:root:Filtering sample
INFO:root:Retrieving cell type information of each sample from DISCO database
Traceback (most recent call last):
  File "D:\Code\PycharmProjects\bio_data_download\disco_down.py", line 45, in <module>
    metadata = down_10x()
  File "D:\Code\PycharmProjects\bio_data_download\disco_down.py", line 8, in down_10x
    metadata = dt.filter_disco_metadata(filter)
  File "D:\Develop\miniconda3\envs\py39\lib\site-packages\discotoolkit\GetMetadata.py", line 228, in filter_disco_metadata
    metadata["cell_number"] = list(sample_cell_count.loc[list(metadata["sampleId"])]["x"]) # assigning to the metadata
  File "D:\Develop\miniconda3\envs\py39\lib\site-packages\pandas\core\indexing.py", line 1073, in __getitem__
    return self._getitem_axis(maybe_callable, axis=axis)
  File "D:\Develop\miniconda3\envs\py39\lib\site-packages\pandas\core\indexing.py", line 1301, in _getitem_axis
    return self._getitem_iterable(key, axis=axis)
  File "D:\Develop\miniconda3\envs\py39\lib\site-packages\pandas\core\indexing.py", line 1239, in _getitem_iterable
    keyarr, indexer = self._get_listlike_indexer(key, axis)
  File "D:\Develop\miniconda3\envs\py39\lib\site-packages\pandas\core\indexing.py", line 1432, in _get_listlike_indexer
    keyarr, indexer = ax._get_indexer_strict(key, axis_name)
  File "D:\Develop\miniconda3\envs\py39\lib\site-packages\pandas\core\indexes\base.py", line 6070, in _get_indexer_strict
    self._raise_if_missing(keyarr, indexer, axis_name)
  File "D:\Develop\miniconda3\envs\py39\lib\site-packages\pandas\core\indexes\base.py", line 6133, in _raise_if_missing
    raise KeyError(f"{not_found} not in index")
KeyError: "['GSM5741306'] not in index"

two weeks ago it was working fine. I don't know where is the problem, my version is discotoolkit 1.1.2. thank you very much!

update DISCOtoolkit_py failure

Hi Mengwei，
Thank you very much for porting DISCO to python! I want to try to use disco_py, but I installed version 1.0.4 through pip, and the download of this version will fail. I tried to install version 1.0.7 locally and online, but I got an error. I don't know what to do.
Best
Mengtian

Gene ID search method excluding common gene names

Thank you very much for your impressive work!
Thank you again for the previous response. Additionally, I have noticed that some gene names are not included in the provided table in the dataset. Could you please help me with methods to obtain the IDs for these genes? For example: RP11-166D19.1, NPPA-AS1-1...

如何获取基因名称对应的ensembl_id

非常感谢你们的工作, 想问一下是否有一份文件描述数据集中基因名称和ensembl_id的对应关系? 或者提供一下方法, 再次感谢.