Mercurial > repos > goeckslab > scimap_mcmicro_to_anndata

annotate anndata_to_csv.py @ 5:b1ead1b7e0aa draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
author goeckslab
date Wed, 11 Jun 2025 22:18:38 +0000
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4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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1 import argparse
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2 import json
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3 import warnings
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5 import scimap as sm
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6 from anndata import read_h5ad
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9 def main(inputs, outfile):
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10 """
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11 Parameters
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12 ---------
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13 inputs : str
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14 File path to galaxy tool parameter.
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15 anndata : str
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16 File path to anndata.
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17 output : str
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18 File path to output.
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19 """
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20 warnings.simplefilter('ignore')
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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22 with open(inputs, 'r') as param_handler:
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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23 params = json.load(param_handler)
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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25 adata = read_h5ad(params['anndata'])
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27 if params['layer'] == 'x':
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28 params['layer'] = None
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4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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30 df = sm.hl.scimap_to_csv(
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31 adata=adata,
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32 layer=params['layer'],
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33 CellID=params['cellid'],
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34 )
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36 df.to_csv(outfile, index=False)
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39 if __name__ == '__main__':
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40 aparser = argparse.ArgumentParser()
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41 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
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42 aparser.add_argument("-e", "--outfile", dest="outfile", required=True)
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43 args = aparser.parse_args()
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45 main(args.inputs, args.outfile)