diff options
| -rw-r--r-- | .gitignore | 2 | ||||
| -rwxr-xr-x | .guix-shell | 2 | ||||
| -rw-r--r-- | gn/data/dataset.scm | 11 | ||||
| -rw-r--r-- | gn/data/genotype.scm | 2 | ||||
| -rw-r--r-- | gn/runner/gemma.scm | 5 | ||||
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 11 |
6 files changed, 18 insertions, 15 deletions
diff --git a/.gitignore b/.gitignore index fb840e4..55bfd36 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,4 @@ BXD.* pheno.txt +GWA.json +K.json diff --git a/.guix-shell b/.guix-shell index 0eb387b..6e68054 100755 --- a/.guix-shell +++ b/.guix-shell @@ -4,4 +4,4 @@ echo "Create a shell to run tools." -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 $* +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 $* diff --git a/gn/data/dataset.scm b/gn/data/dataset.scm index 3d96663..c28cf25 100644 --- a/gn/data/dataset.scm +++ b/gn/data/dataset.scm @@ -1,11 +1,9 @@ (define-module (gn data dataset) - ;; #:use-module (json) #:use-module (ice-9 match) #:use-module (ice-9 format) #:use-module (ice-9 iconv) #:use-module (ice-9 receive) #:use-module (ice-9 string-fun) - ;; #:use-module (gn db sparql) #:use-module (dbi dbi) #:use-module (gn db mysql) #:use-module (gn data group) @@ -16,8 +14,11 @@ dataset-name )) -(define (dataset-name db probesetfreeze-id) +(define (get-dataset db probesetfreeze-id) (dbi-query db (string-append - "select Name2 from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;")) - (assoc-ref (get-row db) "Name2")) + "select Name,Name2,FullName from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;")) + (get-row db)) + +(define (dataset-name db probesetfreeze-id) + (assoc-ref (get-dataset db probesetfreeze-id) "Name")) diff --git a/gn/data/genotype.scm b/gn/data/genotype.scm index a12deee..c7cb63c 100644 --- a/gn/data/genotype.scm +++ b/gn/data/genotype.scm @@ -1,5 +1,5 @@ (define-module (gn data genotype) - ;; #:use-module (json) + #:use-module (json) #:use-module (ice-9 match) #:use-module (ice-9 format) #:use-module (ice-9 iconv) diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index ff70f57..067800e 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -39,6 +39,7 @@ ;; ---- to start GEMMA precompute inside container ;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm - ;; --- First we compute K - (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" )) + ;; --- 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")) ) diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 8588061..2036adc 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -1,10 +1,10 @@ #! Run from base dir with -.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm +. .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm and with some extra paths -.guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- guile -L . -s ./scripts/precompute/precompute-hits.scm +. .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/precompute-hits.scm You may want to forward a mysql port if there is no DB locally @@ -25,7 +25,6 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org ) - ;; potentially you want to test connection with mysql client: ;; ;; mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;" @@ -59,8 +58,8 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org ;; ---- get first available dataset for precompute: ;; @@ order by dataid - recurse - (define (get-trait-name db probeset-id) - (dbi-query db (string-append "select Name,Symbol from ProbeSet where Id=" (int-to-string probeset-id) " limit 1")) + (define (get-trait db probeset-id) + (dbi-query db (string-append "select Id,Chr,Mb,Name,Symbol,description from ProbeSet where Id=" (int-to-string probeset-id) " limit 1")) (get-row db) ) @@ -70,7 +69,7 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org (data-id-str (int-to-string data-id)) (probesetfreeze-id (assoc-ref hit "ProbeSetFreezeId")) (probeset-id (assoc-ref hit "ProbeSetId")) - (trait (get-trait-name db probeset-id)) + (trait (get-trait db probeset-id)) (trait-name (assoc-ref trait "Name")) (name (dataset-name db probesetfreeze-id)) ] |