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Home Page: http://www.immunesinglecell.org/
Python version of DISCO toolkit
Home Page: http://www.immunesinglecell.org/
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!
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...
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.
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