diff options
| -rwxr-xr-x | .guix-shell | 2 | ||||
| -rw-r--r-- | gn/data/population.scm | 28 | ||||
| -rw-r--r-- | gn/runner/gemma.scm | 11 | ||||
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 6 |
4 files changed, 39 insertions, 8 deletions
diff --git a/.guix-shell b/.guix-shell index 6e68054..d5e9c38 100755 --- a/.guix-shell +++ b/.guix-shell @@ -4,4 +4,4 @@ echo "Create a shell to run tools." -guix shell -L ~/guix-bioinformatics -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel tar xz python python-lmdb python-cffi gemma-gn2 $* +guix shell -L ~/guix-bioinformatics -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel tar xz python python-lmdb python-cffi time gemma-gn2 $* diff --git a/gn/data/population.scm b/gn/data/population.scm new file mode 100644 index 0000000..46ef04c --- /dev/null +++ b/gn/data/population.scm @@ -0,0 +1,28 @@ +(define-module (gn data population) + #:use-module (json) + #:use-module (ice-9 match) + #:use-module (ice-9 format) + #:use-module (ice-9 iconv) + #:use-module (ice-9 receive) + #:use-module (ice-9 string-fun) + ;; #:use-module (gn db sparql) + #:use-module (dbi dbi) + #:use-module (gn data group) + #:use-module (gn db mysql) + #:use-module (gn util convert) + #:use-module (web gn-uri) + + #:export ( + population-info + )) + +(define* (population-info id) + " +Return population (InbredSet) info by GN ID +" + (call-with-db + (lambda (db) + (dbi-query db (string-append + "SELECT InbredSetId,InbredSetName,Name,SpeciesId,FullName WHERE" + (int-to-string id) " LIMIT 1")) + (get-row db)))) diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 067800e..d6b08f2 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -12,7 +12,7 @@ run-gemma )) -(define (run-gemma data-id name trait-name traits) +(define (run-gemma population data-id name trait-name traits) (define bxd-inds (geno-inds-bxd "BXD.json")) (assert (= 235 (length bxd-inds))) (if name @@ -40,6 +40,9 @@ ;; ---- to start GEMMA precompute inside container ;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm ;; --- First we compute K - control output goes to K.json - (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --name " name " --trait " trait-name " --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt > K.json" )) - (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --name " name " --trait " trait-name " --verbose --loco --json --debug --parallel --input K.json -- -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt -lmm 2 -maf 0.1 > GWA.json")) - ) + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt > K.json" )))] + (if (not (= err 0)) + (exit err))) + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel --input K.json -- -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt -lmm 2 -maf 0.1 > GWA.json")))] + (if (not (= err 0)) + (exit err)))) diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 2036adc..0fabe8f 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -44,9 +44,9 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org ;(let [(result (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))] ; (display (car result))) - ;(newline) + ;; ---- fetch all known BXD sample/individual/strain names (define bxd-strains (bxd-strain-id-names #:map? #t)) - ;(display (assoc 64728 bxd-strains)) + ;(display (assoc 64728 bxd-strains)) ;(newline) ;(newline) ;(dbi-query db "SELECT * FROM ProbeSetXRef LIMIT 3") @@ -103,7 +103,7 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org (if (eq? non-bxd '()) (begin (set-precompute-hit-status! db data-id-str "GEMMA-START") - (run-gemma data-id name trait-name traits))) + (run-gemma "BXD" data-id name trait-name traits))) ;; disable precompute if non-bxd, for now, so it won't try again (set-precompute-hit-status! db data-id-str "NON-BXD") ;;(run-precompute db data-id) |