Mercurial > repos > goeckslab > scimap_mcmicro_to_anndata

annotate scimap_spatial.py @ 1:8ca435ec19be draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
1 import argparse
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
2 import json
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
3 import warnings
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
4
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
5 import scimap as sm
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
6 from anndata import read_h5ad
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
7
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
8
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
9 def main(inputs, anndata, output):
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
10 """
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
11 Parameter
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
12 ---------
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
13 inputs : str
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
14 File path to galaxy tool parameter.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
15 anndata : str
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
16 File path to anndata containing phenotyping info.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
17 output : str
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
18 File path to output.
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
19 """
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
20 warnings.simplefilter('ignore')
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
21
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
22 with open(inputs, 'r') as param_handler:
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
23 params = json.load(param_handler)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
24
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
25 adata = read_h5ad(anndata)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
26
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
27 tool = params['analyses']['selected_tool']
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
28 tool_func = getattr(sm.tl, tool)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
29
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
30 options = params['analyses']['options']
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
31 if tool == 'cluster':
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
32 options['method'] = params['analyses']['method']
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
33 subset_genes = options.pop('subset_genes')
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
34 if subset_genes:
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
35 options['subset_genes'] = \
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
36 [x.strip() for x in subset_genes.split(',')]
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
37 sub_cluster_group = options.pop('sub_cluster_group')
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
38 if sub_cluster_group:
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
39 options['sub_cluster_group'] = \
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
40 [x.strip() for x in sub_cluster_group.split(',')]
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
41
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
42 for k, v in options.items():
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
43 if v == '':
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
44 options[k] = None
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
45
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
46 tool_func(adata, **options)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
47
1
8ca435ec19be planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit d20d6f5d08b43de71182459f8a6452c564a5becc
goeckslab
parents: 0
diff changeset
48 if tool == 'spatial_lda':
8ca435ec19be planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit d20d6f5d08b43de71182459f8a6452c564a5becc
goeckslab
parents: 0
diff changeset
49 adata.uns.pop('spatial_lda_model')
8ca435ec19be planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit d20d6f5d08b43de71182459f8a6452c564a5becc
goeckslab
parents: 0
diff changeset
50
0
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
51 adata.write(output)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
52
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
53
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
54 if __name__ == '__main__':
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
55 aparser = argparse.ArgumentParser()
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
56 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
57 aparser.add_argument("-e", "--output", dest="output", required=True)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
58 aparser.add_argument("-a", "--anndata", dest="anndata", required=True)
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
59
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
60 args = aparser.parse_args()
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
61
2a3152751ca8 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
parents:
diff changeset
62 main(args.inputs, args.anndata, args.output)