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Teichlab / cellphonedb

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Custom interaction list resulting in KeyError: 'partner_a' #320

Closed sylvia-science closed 3 years ago

sylvia-science commented 3 years ago

Hello,

I'm trying to input my own interaction list. I'm running the following code on it:

cellphonedb database generate --user-interactions interaction_input.csv

I get the resulting error. At first I thought something was wrong with how I inputted my genes, but I tried rerunning with only the first line of the interaction list downloaded from the website but it still gives the same error. File "/Users/u0144780/opt/anaconda3/envs/cpdb/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc raise KeyError(key) from err KeyError: 'partner_a'

Here's the interaction input file. interaction_input.csv

prete commented 3 years ago

Hi @sylvia-science you're using ; as a separator character when you should be using , for csv files. Alternatively you can change ; for \t (TAB) and rename the extension of the file to.tsv

Your file should look like this:

id_cp_interaction,partner_a,partner_b,protein_name_a,protein_name_b,annotation_strategy,source
CPI-CC0041E1D30,IL12,IL12 receptor,,,curated,uniprot