Mercurial > repos > goeckslab > scimap_phenotyping

annotate mcmicro_to_anndata.py @ 0:7ed4b55b11f7 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
author goeckslab
date Tue, 19 Jul 2022 20:29:22 +0000
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children ce22e846c5e4
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
1 import argparse
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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2 import json
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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3 import warnings
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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4
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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5 import scimap as sm
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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8 def main(inputs, outfile):
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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9 """
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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10 Parameter
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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11 ---------
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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12 inputs : str
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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13 File path to galaxy tool parameter.
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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15 outfile : str
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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16 File path to estimator.
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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17 """
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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18 warnings.simplefilter('ignore')
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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19
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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20 with open(inputs, 'r') as param_handler:
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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21 params = json.load(param_handler)
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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23 image_path = params['image_path']
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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24 drop_markers = params['drop_markers']
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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25 if not drop_markers:
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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26 drop_markers = None
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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27 else:
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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28 drop_markers = [x.strip() for x in drop_markers.split(',')]
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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29 options = params['options']
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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30 for k, v in options.items():
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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31 if v == '':
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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32 options[k] = None
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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34 adata = sm.pp.mcmicro_to_scimap(image_path, drop_markers=drop_markers, **options)
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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36 adata.write(outfile)
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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39 if __name__ == '__main__':
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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40 aparser = argparse.ArgumentParser()
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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41 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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42 aparser.add_argument("-e", "--outfile", dest="outfile", required=True)
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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43 args = aparser.parse_args()
7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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7ed4b55b11f7 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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45 main(args.inputs, args.outfile)