Mercurial > repos > gaelcge > r_signac_galaxy

comparison signac-add_gene_annotations.R @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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-1:000000000000 0:6e0b320d8b6a
1 #!/usr/bin/env Rscript
2
3 # Load optparse we need to check inputs
4
5 suppressPackageStartupMessages(require(optparse))
6
7 # Load common functions
8
9 suppressPackageStartupMessages(require(workflowscriptscommon))
10
11 # parse options
12
13 option_list = list(
14 make_option(
15 c("--signac-object"),
16 action = "store",
17 default = NA,
18 type = 'character',
19 help = "Filtered peak BC matrix file in h5 format."
20 ),
21 make_option(
22 c("--ens-db-genome"),
23 action = "store",
24 default = NA,
25 type = 'character',
26 help = "Metadata file."
27 ),
28 make_option(
29 c("--annotations"),
30 action = "store",
31 default = NA,
32 type = 'character',
33 help = "Genome version."
34 ),
35 make_option(
36 c("--output-object-file"),
37 action = "store",
38 default = NA,
39 type = 'character',
40 help = "File name in which to store serialized R matrix object."
41 )
42 )
43
44 opt <- wsc_parse_args(option_list)
45
46 suppressPackageStartupMessages(require(Seurat))
47 suppressPackageStartupMessages(require(Signac))
48 suppressPackageStartupMessages(require(GenomeInfoDb))
49 suppressPackageStartupMessages(require(EnsDb.Hsapiens.v75))
50 suppressPackageStartupMessages(require(EnsDb.Mmusculus.v79))
51
52 set.seed(1234)
53
54 # extract gene annotations from EnsDb
55 signac_object <- readRDS(file = opt$signac_object)
56
57 annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
58 print(annotations)
59
60 # change to UCSC style since the data was mapped to hg19
61 seqlevelsStyle(annotations) <- "UCSC"
62 genome(annotations) <- opt$annotations
63
64 # add the gene information to the object
65 Annotation(signac_object) <- annotations
66
67 print(signac_object)
68
69 # Output to a serialized R object
70 saveRDS(signac_object, file = opt$output_object_file)