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phbradley / conga

Clonotype Neighbor Graph Analysis
MIT License
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Merging with Batch Keys #42

Closed SandwichFiend closed 2 years ago

SandwichFiend commented 2 years ago

Hello,

I'm having trouble merging samples with Batch Keys as described in the ReadMe. I'm trying to execute the following:

Define Batch Keys

BKeys = ["sample"]

Merge the TCR Data

!python /content/conga/scripts/merge_samples.py \ --samples /content/drive/MyDrive/R_Data/Samples.txt \ --output_clones_file merged_pbmc_clones.tsv \ --output_gex_data merged_pbmc_gex.h5ad \ --organism mouse \ --batch_keys BKeys

My samples file is formatted as follows: clones_file gex_data gex_data_type sample /content/S1_clones.tsv /content/drive/MyDrive/R_Data/S1_mtx 10x_mtx 1 /content/S2_clones.tsv /content/drive/MyDrive/R_Data/S2_mtx 10x_mtx 2

This throws the following error: /usr/local/lib/python3.7/dist-packages/statsmodels/tools/_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as tm reading: /content/drive/MyDrive/R_Data/S1_mtx of type 10x_mtx /content/conga/conga/preprocess.py:226: DeprecationWarning: Use is_view instead of isview, isview will be removed in the future. if adata.isview: # ran into trouble with AnnData views vs copies Traceback (most recent call last): File "/content/conga/scripts/merge_samples.py", line 91, in assert k in df.columns AssertionError

This code will complete successfully without the batch keys flag. What am I doing wrong?

Thanks!

SandwichFiend commented 2 years ago

Update: Made 2 changes and it worked.

  1. Changed .txt file to .tsv file
  2. Changed --batch_keys BKeys to --batch_keys 'sample'

I guess it didn't like one of those things.

Thanks for the cool package!