Mercurial > repos > goeckslab > cell_intensity_processing
comparison scale_cell_coordinates.py @ 5:afa3cb2110eb draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
| author | goeckslab |
|---|---|
| date | Thu, 11 Jul 2024 22:41:26 +0000 |
| parents | |
| children |
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| 4:5d541df02496 | 5:afa3cb2110eb |
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| 1 import argparse | |
| 2 import json | |
| 3 import warnings | |
| 4 | |
| 5 import anndata as ad | |
| 6 | |
| 7 | |
| 8 def main(inputs, output): | |
| 9 | |
| 10 """ | |
| 11 inputs : str | |
| 12 File path to galaxy tool JSON inputs config file | |
| 13 output: str | |
| 14 File path to save the output h5ad file | |
| 15 """ | |
| 16 warnings.simplefilter('ignore') | |
| 17 | |
| 18 # read inputs JSON | |
| 19 with open(inputs, 'r') as param_handler: | |
| 20 params = json.load(param_handler) | |
| 21 | |
| 22 # read input anndata file | |
| 23 adata = ad.read_h5ad(params['anndata']) | |
| 24 | |
| 25 # scale coords | |
| 26 unit = params['unit'] | |
| 27 new_col_names = [] | |
| 28 for c in [params['x_coord'], params['y_coord']]: | |
| 29 scaled_col_name = f'{c}_{unit}' | |
| 30 adata.obs[scaled_col_name] = adata.obs[c] * params['resolution'] | |
| 31 new_col_names.append(scaled_col_name) | |
| 32 | |
| 33 # overwrite adata.obsm['spatial'] with scaled coordinates | |
| 34 adata.obsm['spatial'] = adata.obs[scaled_col_name].values | |
| 35 | |
| 36 # write out anndata to h5ad file | |
| 37 adata.write_h5ad(output) | |
| 38 | |
| 39 | |
| 40 if __name__ == '__main__': | |
| 41 | |
| 42 aparser = argparse.ArgumentParser() | |
| 43 aparser.add_argument( | |
| 44 "-i", "--inputs", dest="inputs", required=True) | |
| 45 aparser.add_argument( | |
| 46 "-o", "--output", dest="output", required=False) | |
| 47 | |
| 48 args = aparser.parse_args() | |
| 49 | |
| 50 main(args.inputs, args.output) |