Trainer AssertionError

[Ricardo Guerreiro]

I can't overcome this assertion error:

~/.local/lib/python3.8/site-packages/deepsort/trainer.py in __load_train_data(self, files, save_dir)
    239             # filter out cells not in label-text
    240             df = df.iloc[filter_cell]
--> 241             assert cell2type['cell'].tolist() == df.index.tolist()
    242             df = df.rename(columns=gene2id)
    243             # filter out useless columns if exists (when using gene intersection)

AssertionError: 

This is probably because my input data does not perfectly match the format that it expects. How do the tutorial files ('/path/to/human_brain_data_1.csv', '/path/to/human_brain_celltype_1.csv') exactly look like?

Here are my inputs:

x_train.iloc[:,:3]

cell	8194	6001	4401
CD4	0.0	0.293348	0.0
DCN	0.0	0.157392	0.0
...	...	...
FCGBP	0.0	0.000000	0.0
GJA5	0.0	0.000000	0.0

95 rows × 5584 columns

	cell	type	id
8090	8194	t-cells	0
5921	6001	kupffer cells	2
...	...	...
860	862	kupffer cells	2
7270	7360	hepatic stellate cells	7

5584 rows × 3 columns

Thank you,

[Ricardo Guerreiro]

Solved it with 2 things:
Replaced the columns of the first table with the corresponding value/name of cell in the 2nd table.
Added a line to your code, before the assertion, to force cell names to be strings, as mine were interpreted as integers.

~/.local/lib/python3.8/site-packages/deepsort/trainer.py

--->243 cell2type['cell'] = cell2type['cell'].map(str)