Open yeroslaviz opened 5 years ago
But when running the command with the new data I still get an error
wot optimal_transport --matrix data/ExprMatrix.h5ad --cell_days data/cell_days.txt --out tmaps1.0.2/tmaps1.0.2
the files are as followed
data/ExprMatrix.h5ad
id Xkr4 Sox17 Mrpl15 Lypla1 ...
D0_Dox_C1_AAACCTGAGTATCTCG-1 0.0 0.0 0.98459476 0.0 ...
D0_Dox_C1_AAACCTGCAAGCGAGT-1 0.0 0.0 0.7069785 0.0 ...
...
data/cell_days.txt
D0_Dox_C1_AAACCTGAGTATCTCG-1 0
D0_Dox_C1_AAACCTGCAAGCGAGT-1 0
D0_Dox_C1_AAACCTGGTCTCTTAT-1 0
But the error calims the day information is not available for that:
Traceback (most recent call last):
File "/home/yeroslaviz/miniconda3/envs/Waddington/bin/wot", line 11, in <module>
load_entry_point('wot', 'console_scripts', 'wot')()
File "/home/yeroslaviz/miniconda3/envs/Waddington/lib/python3.7/site-packages/wot/wot/__main__.py", line 23, in main
cmd.main(command_args)
File "/home/yeroslaviz/miniconda3/envs/Waddington/lib/python3.7/site-packages/wot/wot/commands/optimal_transport.py", line 23, in main
ot_model = wot.commands.initialize_ot_model_from_args(args)
File "/home/yeroslaviz/miniconda3/envs/Waddington/lib/python3.7/site-packages/wot/wot/commands/util.py", line 47, in initialize_ot_model_from_args
covariate=args.covariate if hasattr(args, 'covariate') else None
File "/home/yeroslaviz/miniconda3/envs/Waddington/lib/python3.7/site-packages/wot/wot/ot/initializer.py", line 39, in initialize_ot_model
return OTModel(ds, **kwargs)
File "/home/yeroslaviz/miniconda3/envs/Waddington/lib/python3.7/site-packages/wot/wot/ot/ot_model.py", line 111, in __init__
raise ValueError("Days information not available for matrix")
ValueError: Days information not available for matrix
After installing version 1.0.2 and running the command
I get the following error
I have bin able to temporarily fix it by downgrading
scipy
to version 1.2.1 inside my conda environment.