How to create user's own database with a new interaction list file??

[Sara0201Tao]

Hi ,

Thank you very much for this package. After trying the default database, I have some new LR interaction pairs from literatures and want to creat a new database to test. Unfortunately, I came across to some problems and don’t know how to slove it. what I want to is, what file and what format should I prepare for the command [cellphonedb database generate]?

The command what I wrote is : cellphonedb database generate --user-interactions CellP_italk_LR.csv --user-interactions-only

the CellP_italk_LR.csv looks like this:

and the results and error it returns is as follows: [ ][APP][01/12/20-12:02:22][WARNING] Output directory (/home/mztao/cellp_test/new_database/out) exist and is not empty. Result can overwrite old results read local ensembl file read local uniprot file /home/mztao/cellp_test/lib/python3.7/site-packages/cellphonedb/src/core/generators/gene_generator.py:31: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy ensembl_db_filtered.dropna(inplace=True) [ ][APP][01/12/20-12:02:38][WARNING] Output directory (/home/mztao/cellp_test/new_database/out) exist and is not empty. Result can overwrite old results [ ][APP][01/12/20-12:02:38][WARNING] Output directory (/home/mztao/cellp_test/new_database/out) exist and is not empty. Result can overwrite old results [ ][APP][01/12/20-12:02:38][WARNING] Output directory (/home/mztao/cellp_test/new_database/out) exist and is not empty. Result can overwrite old results [ ][APP][01/12/20-12:02:38][WARNING] Output directory (/home/mztao/cellp_test/new_database/out) exist and is not empty. Result can overwrite old results [ ][APP][01/12/20-12:02:39][WARNING] Output directory (/home/mztao/cellp_test/new_database/out) exist and is not empty. Result can overwrite old results Traceback (most recent call last): File "/home/mztao/cellp_test/bin/cellphonedb", line 11, in sys.exit(cli()) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/core.py", line 722, in call return self.main(args, kwargs) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/core.py", line 697, in main rv = self.invoke(ctx) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/core.py", line 895, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/core.py", line 535, in invoke return callback(args, kwargs) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/decorators.py", line 17, in new_func return f(get_current_context(), *args, *kwargs) File "/home/mztao/cellp_test/lib/python3.7/site-packages/cellphonedb/src/api_endpoints/terminal_api/database_terminal_api_endpoints/database_terminal_commands.py", line 105, in generate ctx.invoke(filter_all, input_path=output_path, result_path=result_path) File "/home/mztao/cellp_test/lib/python3.7/site-packages/click/core.py", line 535, in invoke return callback(args, kwargs) File "/home/mztao/cellp_test/lib/python3.7/site-packages/cellphonedb/src/api_endpoints/terminal_api/tools_terminal_api_endpoints/tools_terminal_commands.py", line 342, in filter_all ', '.join(rejected_members))) TypeError: sequence item 705: expected str instance, float foun

Thanks for your time and llok forward to you reply~

Sara

[martin-jeremy]

+1

[luzgaral]

I recommend you to use uniprot ids, like in the original file: https://raw.githubusercontent.com/Teichlab/cellphonedb-data/master/data/sources/interaction_curated.csv

Check CellPhoneDB Lists Curated https://www.cellphonedb.org/downloads for examples of file formats to generate the database