Mercurial > repos > goeckslab > scimap_mcmicro_to_anndata

annotate anndata_to_csv.py @ 3:8c55377d7f06 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 49210b00535415865694ddbec16238d8cf5e6bb0
author goeckslab
date Wed, 26 Jun 2024 15:27:13 +0000
parents 4c767e1a9e7c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
1 import argparse
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
2 import json
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
3 import warnings
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
4
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
5 import scimap as sm
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
6 from anndata import read_h5ad
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
7
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
8
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
9 def main(inputs, outfile):
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
10 """
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
11 Parameters
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
12 ---------
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
13 inputs : str
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
14 File path to galaxy tool parameter.
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
15 anndata : str
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
16 File path to anndata.
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
17 output : str
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
18 File path to output.
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
19 """
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
20 warnings.simplefilter('ignore')
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
21
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
22 with open(inputs, 'r') as param_handler:
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
23 params = json.load(param_handler)
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
24
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
25 adata = read_h5ad(params['anndata'])
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
26
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
27 if params['layer'] == 'x':
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
28 params['layer'] = None
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
29
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
30 df = sm.hl.scimap_to_csv(
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
31 adata=adata,
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
32 layer=params['layer'],
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
33 CellID=params['cellid'],
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
34 )
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
35
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
36 df.to_csv(outfile, index=False)
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
37
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
38
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
39 if __name__ == '__main__':
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
40 aparser = argparse.ArgumentParser()
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
41 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
42 aparser.add_argument("-e", "--outfile", dest="outfile", required=True)
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
43 args = aparser.parse_args()
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
44
4c767e1a9e7c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
parents:
diff changeset
45 main(args.inputs, args.outfile)