Mercurial > repos > goeckslab > scimap_phenotyping

comparison scimap_phenotyping.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
parents
children ce22e846c5e4
comparison
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-1:000000000000 0:7ed4b55b11f7
1 import argparse
2 import warnings
3
4 import pandas as pd
5 import scimap as sm
6 from anndata import read_h5ad
7
8
9 def main(
10 adata,
11 output,
12 gating_workflow,
13 gating_workflow_ext,
14 manual_gates=None,
15 manual_gates_ext=None,
16 rescale_plots=False
17 ):
18 """
19 Parameter
20 ---------
21 adata : str
22 File path to the input AnnData.
23 output : str
24 File path to the output AnnData.
25 gating_workflow : str
26 File path to the gating workflow.
27 gating_workflow_ext : str
28 Datatype for gating workflow, either 'csv' or 'tabular'.
29 manual_gates : str
30 File path to the munual gating.
31 manual_gates_ext : str
32 Datatype for munual gate, either 'csv' or 'tabular'.
33 rescale_plots : boolean
34 Save plots from rescaling.
35 """
36 warnings.simplefilter('ignore')
37
38 adata = read_h5ad(adata)
39 # Rescale data
40 if manual_gates:
41 sep = ',' if manual_gates_ext == 'csv' else '\t'
42 manual_gates = pd.read_csv(manual_gates, sep=sep)
43
44 adata = sm.pp.rescale(adata, gate=manual_gates, save_fig=rescale_plots)
45
46 # Phenotype cells
47 # Load the gating workflow
48 sep = ',' if gating_workflow_ext == 'csv' else '\t'
49 phenotype = pd.read_csv(gating_workflow, sep=sep)
50 adata = sm.tl.phenotype_cells(adata, phenotype=phenotype, label="phenotype")
51
52 # Summary of the phenotyping
53 print(adata.obs['phenotype'].value_counts())
54
55 adata.write(output)
56
57
58 if __name__ == '__main__':
59 aparser = argparse.ArgumentParser()
60 aparser.add_argument("-a", "--adata", dest="adata", required=True)
61 aparser.add_argument("-o", "--output", dest="output", required=True)
62 aparser.add_argument("-g", "--gating_workflow", dest="gating_workflow", required=True)
63 aparser.add_argument("-s", "--gating_workflow_ext", dest="gating_workflow_ext", required=True)
64 aparser.add_argument("-m", "--manual_gates", dest="manual_gates", required=False)
65 aparser.add_argument("-S", "--manual_gates_ext", dest="manual_gates_ext", required=False)
66 aparser.add_argument("-p", "--rescale_plots", dest="rescale_plots", action="store_true",
67 default=False, required=False)
68
69 args = aparser.parse_args()
70
71 main(args.adata, args.output, args.gating_workflow,
72 args.gating_workflow_ext, args.manual_gates,
73 args.manual_gates_ext, args.rescale_plots)