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seurattoadata's Introduction

Convert Seurat Obj (rds) to Scanpy obj (adata)

Usage:

conda enve create -f env.yaml
conda activate seuratToAdata

usage: seuratToAdata [-h] -o OUTPUT [--RNA] rds

positional arguments:
  rds                   Use - for STDIN or path for seurat obj(*.rds file)

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Specify path to write the results (default: None)
  --RNA                 Whether is store in the RNA slot (default: False)

Issues might arise:

  1. UnicodeDecodeError: 'ascii' codec can't decode byte 0xcf in position 1: ordinal not in range(128).

    Solved by fixing the locale: https://stackoverflow.com/questions/51026315/how-to-solve-unicodedecodeerror-in-python-3-6/51027262#51027262

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