diff --git a/scripts/data/data.sh b/scripts/data/data.sh index fe1f706..bcad283 100755 --- a/scripts/data/data.sh +++ b/scripts/data/data.sh @@ -95,6 +95,10 @@ clearConfs # ./biobtree -d hgnc --idx cacheset1 update # prepCache "set1" +### CACHE 0 small demo dataset for biobtreeR ~ 36 MB db size +./biobtree -d go,hgnc,uniprot,ensembl,interpro --uniprot.file ../../test_data/RdemoData/uniprot_sample.xml.gz --interpro.file ../../test_data/RdemoData/interpro_sample.xml.gz --ensembl.file ../../test_data/RdemoData/human.chr.21.gff3.gz --go.file ../../test_data/RdemoData/go_sample.owl -tax 9606 -idx demo update +prepCache "demo" "36000000" + ### CACHE 1 datasets with above ensembl genomes except mouse strains. ~ 5.2 db size ./biobtree -d hgnc,hmdb,uniprot,taxonomy,go,efo,eco,chebi,interpro -tax 9606,10090,4932,3702,7227,6239,562,511145,83333,7955,9031,10116 -x --skip-ensembl -idx cacheset1 update @@ -110,5 +114,4 @@ prepCache "set2" "4100000000" ./biobtree -d hgnc,hmdb,uniprot,taxonomy,go,efo,eco,chebi,interpro -x -idx cacheset3 update prepCache "set3" "3600000000" - clearConfs diff --git a/scripts/release.bat b/scripts/release.bat index a349310..e6c93b9 100644 --- a/scripts/release.bat +++ b/scripts/release.bat @@ -10,4 +10,4 @@ IF EXIST [biobtree_Windwos_64bit.zip] ( go build -7z.exe a biobtree_Windwos_64bit.zip biobtree.exe \ No newline at end of file +7z.exe a biobtree_Windows_64bit.zip biobtree.exe \ No newline at end of file diff --git a/update/update.go b/update/update.go index 64923ac..a972dba 100755 --- a/update/update.go +++ b/update/update.go @@ -113,6 +113,10 @@ func NewDataUpdate(datasets map[string]bool, targetDatasets, ensemblSpecies, ens } } + if orthologsAll { + orthologs = true + } + return &DataUpdate{ invalidXrefs: util.NewHashMap(300), sampleXrefs: util.NewHashMap(400),