diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rwxr-xr-x | .guix-shell | 2 | ||||
| -rw-r--r-- | gn/runner/gemma.scm | 20 | ||||
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 22 |
4 files changed, 31 insertions, 14 deletions
diff --git a/.gitignore b/.gitignore index 047b170..fb840e4 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ BXD.* +pheno.txt diff --git a/.guix-shell b/.guix-shell index 988e529..f3c4ebc 100755 --- a/.guix-shell +++ b/.guix-shell @@ -4,4 +4,4 @@ echo "Create a shell to run tools. In the container" -guix shell -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 $* +guix shell -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 $* diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 67dae54..ff70f57 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -23,14 +23,22 @@ ;; ---- write phenotype file (call-with-output-file "pheno.txt" (lambda (port) - (write 12 port) - (newline port) - (write "HELLO" port) - )) + (for-each (lambda (ind) + (begin + (let* [(value (assoc-ref traits ind)) + (outvalue (if value + value + "NA"))] + (display outvalue) + (newline) + (display outvalue port) + (newline port)))) + bxd-inds))) + ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm ;; ---- to start GEMMA precompute inside container - ;; env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm + ;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm ;; --- First we compute K - (system (string-append "env GEMMA_COMMAND=/gemma/bin/gemma /gemma-wrapper/bin/gemma-wrapper --debug -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt" )) + (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt" )) ) diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index b9dd746..8762a6a 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -11,7 +11,7 @@ (gn data strains) (gn util convert) (gn runner gemma) - (rnrs base) + ; (rnrs base) (ice-9 match) (srfi srfi-1) ) @@ -64,26 +64,34 @@ (probeset-id (assoc-ref hit "ProbeSetId")) (trait (get-trait-name db probeset-id)) (trait-name (assoc-ref trait "Name")) + (name (dataset-name db probesetfreeze-id)) ] (display hit) (display data-id) (newline) - (define name (dataset-name db probesetfreeze-id)) ;; ---- Get strains and phenotypes for this dataset (dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" data-id-str)) - (define traits (get-rows-apply db + (define id_traits (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "value"))) '())) ;; ---- Now we need to make sure that all strains belong to BXD (define non-bxd (fold (lambda (strain lst) - (let ([id (car strain)]) - (if (assoc id bxd-strains) + (let* [(id (car strain)) + (name (assoc id bxd-strains))] + (if name lst - (append lst `(,id))))) + (append lst `(,name))))) '() - traits)) + id_traits)) + (define traits (map + (lambda (t) + (match t + ((id . value) (cons (assoc-ref bxd-strains id) value) + ))) + id_traits)) + (display traits) ;; (if (= 0 (length non-bxd)) (if (eq? non-bxd '()) (begin |