Mercurial > repos > goeckslab > scimap_phenotyping
annotate mcmicro_to_anndata.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 | 7ed4b55b11f7 |
| children |
| rev | line source |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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1 import argparse |
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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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2 import json |
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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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changeset
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3 import warnings |
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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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4 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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5 import scimap as sm |
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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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6 |
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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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7 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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8 def main(inputs, outfile): |
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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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9 """ |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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10 Parameter |
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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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11 --------- |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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12 inputs : str |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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13 File path to galaxy tool parameter. |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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14 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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15 outfile : str |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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16 File path to estimator. |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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17 """ |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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18 warnings.simplefilter('ignore') |
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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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19 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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20 with open(inputs, 'r') as param_handler: |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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21 params = json.load(param_handler) |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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22 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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23 image_path = params['image_path'] |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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24 drop_markers = params['drop_markers'] |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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25 if not drop_markers: |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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26 drop_markers = None |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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27 else: |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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28 drop_markers = [x.strip() for x in drop_markers.split(',')] |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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29 options = params['options'] |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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30 for k, v in options.items(): |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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31 if v == '': |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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32 options[k] = None |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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33 |
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2
ce22e846c5e4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
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diff
changeset
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34 adata = sm.pp.mcmicro_to_scimap( |
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ce22e846c5e4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
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changeset
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35 image_path, |
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ce22e846c5e4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
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diff
changeset
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36 drop_markers=drop_markers, |
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ce22e846c5e4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
0
diff
changeset
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37 **options |
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ce22e846c5e4
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
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38 ) |
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0
7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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39 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
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changeset
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40 adata.write(outfile) |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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41 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
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42 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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43 if __name__ == '__main__': |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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44 aparser = argparse.ArgumentParser() |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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45 aparser.add_argument("-i", "--inputs", dest="inputs", required=True) |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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46 aparser.add_argument("-e", "--outfile", dest="outfile", required=True) |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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47 args = aparser.parse_args() |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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48 |
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7ed4b55b11f7
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff
changeset
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49 main(args.inputs, args.outfile) |