Mercurial > repos > goeckslab > scimap_phenotyping
comparison anndata_to_csv.py @ 2:ce22e846c5e4 draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
| author | goeckslab |
|---|---|
| date | Mon, 10 Jun 2024 18:44:25 +0000 |
| parents | |
| children |
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| 1:dcfcad35e847 | 2:ce22e846c5e4 |
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| 1 import argparse | |
| 2 import json | |
| 3 import warnings | |
| 4 | |
| 5 import scimap as sm | |
| 6 from anndata import read_h5ad | |
| 7 | |
| 8 | |
| 9 def main(inputs, outfile): | |
| 10 """ | |
| 11 Parameters | |
| 12 --------- | |
| 13 inputs : str | |
| 14 File path to galaxy tool parameter. | |
| 15 anndata : str | |
| 16 File path to anndata. | |
| 17 output : str | |
| 18 File path to output. | |
| 19 """ | |
| 20 warnings.simplefilter('ignore') | |
| 21 | |
| 22 with open(inputs, 'r') as param_handler: | |
| 23 params = json.load(param_handler) | |
| 24 | |
| 25 adata = read_h5ad(params['anndata']) | |
| 26 | |
| 27 if params['layer'] == 'x': | |
| 28 params['layer'] = None | |
| 29 | |
| 30 df = sm.hl.scimap_to_csv( | |
| 31 adata=adata, | |
| 32 layer=params['layer'], | |
| 33 CellID=params['cellid'], | |
| 34 ) | |
| 35 | |
| 36 df.to_csv(outfile, index=False) | |
| 37 | |
| 38 | |
| 39 if __name__ == '__main__': | |
| 40 aparser = argparse.ArgumentParser() | |
| 41 aparser.add_argument("-i", "--inputs", dest="inputs", required=True) | |
| 42 aparser.add_argument("-e", "--outfile", dest="outfile", required=True) | |
| 43 args = aparser.parse_args() | |
| 44 | |
| 45 main(args.inputs, args.outfile) |