diff options
| -rw-r--r-- | gn/runner/gemma.scm | 17 | ||||
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 21 |
2 files changed, 23 insertions, 15 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 69991dd..9207316 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -39,24 +39,27 @@ )) ) -(define (invoke-gemma-wrapper-loco name trait-name pheno-fn) +(define (invoke-gemma-wrapper-loco name trait-name trait-fn pheno-fn) "Create a tmpdir and invoke gemma-wrapper using parallel LOCO. Note that at this point we use a number of defaults for BXD" (let* [(population "BXD") (sys-tmpdir (getenv "TMPDIR")) (tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX"))) (k-json-fn (string-append tmpdir "/K.json")) - (gwa-json-fn (string-append tmpdir "/GWA.json"))] + (gwa-json-fn (string-append tmpdir "/GWA.json")) + (trait-json-fn (string-append tmpdir "/" trait-fn))] + (copy-file trait-fn trait-json-fn) ;; --- First we compute K - control output goes to K.json (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --verbose --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))] (if (not (= err 0)) (exit err))) - (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))] + (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --meta \"" trait-json-fn "\" --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --lmdb --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))] (if (not (= err 0)) (exit err))) - ;; (delete-file pheno-fn) - ;; (delete-file gwa-json-fn) - ;; (delete-file k-json-fn) - ;; (rmdir tmpdir) + (delete-file pheno-fn) + (delete-file gwa-json-fn) + (delete-file k-json-fn) + (delete-file trait-json-fn) + (rmdir tmpdir) ) ) diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm index e6a4e26..9a7bba2 100755 --- a/scripts/precompute/run-gemma.scm +++ b/scripts/precompute/run-gemma.scm @@ -39,15 +39,20 @@ and with some extra paths (for gemma) Usage: list-traits-to-compute [options...] -h, --help Display this help ")) - (let [(trait-name "115475")] - (call-with-input-file "115475.json" + (let [(trait-id "115475") + (trait-fn "115475.json") + ] + + (call-with-input-file trait-fn (lambda (port) (let* [(json (json->scm port)) - (dataset (assoc-ref json "traits")) - (dataset-name (car (car dataset))) - (traits (assoc-ref dataset dataset-name)) + (dataset (car (assoc-ref json "data"))) + (data (cdr dataset)) + (dataset-name (assoc-ref data "name")) + (trait-name (assoc-ref data "trait-name")) + (traits (assoc-ref data "traits")) + (pheno-fn (string-append trait-id "-pheno.txt")) ] - (display dataset) - (write-pheno-file "pheno.txt" traits) - (invoke-gemma-wrapper-loco dataset-name trait-name "pheno.txt") + (write-pheno-file pheno-fn traits) + (invoke-gemma-wrapper-loco dataset-name trait-name trait-fn pheno-fn) )))))) |