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STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
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data.tl.cell_cell_communication() #198

Closed Biomamba closed 9 months ago

Biomamba commented 10 months ago

When I run data.tl.cell_cell_communication( analysis_type='statistical', cluster_res_key='leiden', species='MOUSE', database='cellphonedb', res_key='cell_cell_communication' ). The following error ocurred.

File ~/miniconda3/envs/st13/lib/python3.8/site-packages/SQLAlchemy-1.3.24-py3.8-linux-x86_64.egg/sqlalchemy/engine/strategies.py:114, in DefaultEngineStrategy.create.<locals>.connect(connection_record)
    112         if connection is not None:
    113             return connection
--> 114 return dialect.connect(*cargs, **cparams)

File ~/miniconda3/envs/st13/lib/python3.8/site-packages/SQLAlchemy-1.3.24-py3.8-linux-x86_64.egg/sqlalchemy/engine/default.py:508, in DefaultDialect.connect(self, *cargs, **cparams)
    506 def connect(self, *cargs, **cparams):
    507     # inherits the docstring from interfaces.Dialect.connect
--> 508     return self.dbapi.connect(*cargs, **cparams)

OperationalError: (sqlite3.OperationalError) unable to open database file
(Background on this error at: http://sqlalche.me/e/13/e3q8)

my stereopy version is 0.14.0b1. Could you please tell me how to solve it? Is there the way to pre-download the database to avoid the connect error?

tanliwei-coder commented 10 months ago

Did you install stereopy by conda? And also, you can download the database from database

Biomamba commented 10 months ago

Did you install stereopy by conda? And also, you can download the database from database

I'm sure that I have install stereopy and the chapter before this function. Moreover, there are cellphonedb.db, liana.db, celltalkdb.db files in my device. Cloud you please tell me how to solve this problem.

tanliwei-coder commented 10 months ago

I never met this error, could you provide your data to me to try?