list-traits handle CLI options --start-id and --next

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)
+)))