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annotate scimap_phenotyping.py @ 1:8ca435ec19be draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit d20d6f5d08b43de71182459f8a6452c564a5becc
author goeckslab
date Mon, 29 Aug 2022 23:54:52 +0000
parents 2a3152751ca8
children 4c767e1a9e7c
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2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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diff changeset
1 import argparse
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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2 import warnings
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3
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4 import pandas as pd
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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5 import scimap as sm
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6 from anndata import read_h5ad
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7
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8
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9 def main(
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10 adata,
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11 output,
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12 gating_workflow,
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13 gating_workflow_ext,
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14 manual_gates=None,
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15 manual_gates_ext=None,
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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16 rescale_plots=False
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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17 ):
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goeckslab
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18 """
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goeckslab
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19 Parameter
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20 ---------
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21 adata : str
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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22 File path to the input AnnData.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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23 output : str
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goeckslab
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24 File path to the output AnnData.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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25 gating_workflow : str
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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26 File path to the gating workflow.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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27 gating_workflow_ext : str
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28 Datatype for gating workflow, either 'csv' or 'tabular'.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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29 manual_gates : str
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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30 File path to the munual gating.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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31 manual_gates_ext : str
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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32 Datatype for munual gate, either 'csv' or 'tabular'.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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33 rescale_plots : boolean
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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34 Save plots from rescaling.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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35 """
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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36 warnings.simplefilter('ignore')
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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37
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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38 adata = read_h5ad(adata)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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39 # Rescale data
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40 if manual_gates:
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41 sep = ',' if manual_gates_ext == 'csv' else '\t'
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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42 manual_gates = pd.read_csv(manual_gates, sep=sep)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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43
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44 adata = sm.pp.rescale(adata, gate=manual_gates, save_fig=rescale_plots)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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45
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46 # Phenotype cells
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47 # Load the gating workflow
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48 sep = ',' if gating_workflow_ext == 'csv' else '\t'
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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49 phenotype = pd.read_csv(gating_workflow, sep=sep)
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50 adata = sm.tl.phenotype_cells(adata, phenotype=phenotype, label="phenotype")
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51
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52 # Summary of the phenotyping
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53 print(adata.obs['phenotype'].value_counts())
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54
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55 adata.write(output)
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57
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58 if __name__ == '__main__':
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59 aparser = argparse.ArgumentParser()
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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60 aparser.add_argument("-a", "--adata", dest="adata", required=True)
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61 aparser.add_argument("-o", "--output", dest="output", required=True)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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62 aparser.add_argument("-g", "--gating_workflow", dest="gating_workflow", required=True)
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63 aparser.add_argument("-s", "--gating_workflow_ext", dest="gating_workflow_ext", required=True)
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64 aparser.add_argument("-m", "--manual_gates", dest="manual_gates", required=False)
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65 aparser.add_argument("-S", "--manual_gates_ext", dest="manual_gates_ext", required=False)
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66 aparser.add_argument("-p", "--rescale_plots", dest="rescale_plots", action="store_true",
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67 default=False, required=False)
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68
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69 args = aparser.parse_args()
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70
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71 main(args.adata, args.output, args.gating_workflow,
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72 args.gating_workflow_ext, args.manual_gates,
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73 args.manual_gates_ext, args.rescale_plots)