blob: e6a4e26cf5eb2e5afd112452e0d613ac3feede8e (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
|
#! Run GEMMA
A simple script that takes the JSON input from list-traits-to-compute and runs
GEMMA on those.
Run from base dir with
~/opt/guix-pull/bin/guix shell guile guile-dbi guile-json -- guile -L . -e main -s scripts/precompute/run-gemma.scm 115476.json
and with some extra paths (for gemma)
~/opt/guix-pull/bin/guix shell -C -F xz tar time parallel coreutils-minimal guile guile-dbi guile-json ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp GEMMA_COMMAND=/gemma/bin/gemma-0.98.5-linux-static-debug guile -L . -e main -s ./scripts/precompute/run-gemma.scm
!#
(use-modules ; (gn data dataset)
; (gn data hits)
; (gn data strains)
; (gn util convert)
(gn runner gemma)
(ice-9 getopt-long)
(ice-9 match)
(ice-9 textual-ports)
(json)
(rnrs bytevectors)
(srfi srfi-1)
)
(define (main args)
;; (write args)
(let* [
(option-spec '( (version (single-char #\v) (value #f))
(help (single-char #\h) (value #f))))
(options (getopt-long args option-spec))
(help-wanted (option-ref options 'help #f))]
(display "RUNNING")
(if help-wanted
(format #t "list-traits-to-compute writes JSON traits files from the GN DB
Usage: list-traits-to-compute [options...]
-h, --help Display this help
"))
(let [(trait-name "115475")]
(call-with-input-file "115475.json"
(lambda (port)
(let* [(json (json->scm port))
(dataset (assoc-ref json "traits"))
(dataset-name (car (car dataset)))
(traits (assoc-ref dataset dataset-name))
]
(display dataset)
(write-pheno-file "pheno.txt" traits)
(invoke-gemma-wrapper-loco dataset-name trait-name "pheno.txt")
))))))
|
