diff options
Diffstat (limited to 'scripts')
| -rwxr-xr-x | scripts/precompute/list-traits-to-compute.scm | 36 |
1 files changed, 30 insertions, 6 deletions
diff --git a/scripts/precompute/list-traits-to-compute.scm b/scripts/precompute/list-traits-to-compute.scm index e954b14..0bcef3e 100755 --- a/scripts/precompute/list-traits-to-compute.scm +++ b/scripts/precompute/list-traits-to-compute.scm @@ -1,4 +1,5 @@ -#! +#!/usr/bin/env guile \ +-e main -s Step p1 lists traits that need to be computed. @@ -33,7 +34,7 @@ you should see Now list the next 1000 trait IDs: - . .guix-shell -- guile -L . -s ./scripts/precompute/list-traits-to-compute.scm --next 1000 + . .guix-shell -- guile -L . -s ./scripts/precompute/list-traits-to-compute.scm --first 0 --next 1000 The current logic is to list all datasets that contain a BXD. (bxd-strain-id-names #:used-for-mapping? #t) fetches all ids and @@ -66,13 +67,15 @@ When that is the case we might as well write the phenotype file because we have (gn util convert) (gn runner gemma) ; (rnrs base) + (ice-9 getopt-long) (ice-9 match) (srfi srfi-1) ) -(call-with-db - (lambda (db) +(define (write-phenotypes first-id count) + (call-with-db + (lambda (db) (begin (let [(bxd-strains (memo-bxd-strain-id-names #:used-for-mapping? #t))] (define (run-list-traits-to-compute db prev-id count) @@ -110,6 +113,27 @@ When that is the case we might as well write the phenotype file because we have )) nrecs) ; (display nrecs) ))) - (run-list-traits-to-compute db 0 1000) ;; start precompute + (run-list-traits-to-compute db first-id count) ;; start precompute ;; (write bxd-strains) - )))) + ))))) + + +(define (main args) + ;; (write args) + (let* ((option-spec '( (version (single-char #\v) (value #f)) + (start-id (single-char #\s) (value #t)) + (next (single-char #\n) (value #t)) + (help (single-char #\h) (value #f)))) + (options (getopt-long args option-spec)) + (start-id (string->number (option-ref options 'start-id "0"))) + (next (string->number (option-ref options 'next "5"))) + (help-wanted (option-ref options 'help #f))) + (if help-wanted + (format #t "list-traits-to-compute writes JSON traits files from the GN DB +Usage: list-traits-to-compute [options...] + -s, --start-id num Start from ID (default 0) + -n, --next count In batches of count size (default 5) + -h, --help Display this help +") + (write-phenotypes start-id next) +))) |