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tille pushed a commit to branch master
in repository r-bioc-genomeinfodbdata.
commit 6385a397a5421053d5a193224cd243c9a81cb60e
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 10 10:39:29 2017 +0100
New upstream version 0.99.1
---
DESCRIPTION | 8 +++++---
data/datalist | 3 +++
data/specData.rda | Bin 7044532 -> 8201060 bytes
data/speciesMap.rda | Bin 8772520 -> 9295004 bytes
data/validTaxIds.rda | Bin 416192 -> 443484 bytes
inst/scripts/updateGenomeInfoDbData.R | 5 +++--
6 files changed, 11 insertions(+), 5 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index b12ffd9..4735e28 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,12 @@
-Package: GenomeInfoDbData
-Title: Species and taxonomy ID look up tables used by GenomeInfoDb
+Package: GenomeInfoDbData
+Title: Species and taxonomy ID look up tables used by GenomeInfoDb
Description: Files for mapping between NCBI taxonomy ID and species. Used
by functions in the GenomeInfoDb package.
-Version: 0.99.0
+Version: 0.99.1
Author: Bioconductor Core Team
Maintainer: Bioconductor Maintainer <maintainer at bioconductor.org>
Depends: R (>= 3.3)
biocViews: AnnotationData, Organism
License: Artistic-2.0
+NeedsCompilation: no
+Packaged: 2017-10-26 14:18:36 UTC; da42327_ca
diff --git a/data/datalist b/data/datalist
new file mode 100644
index 0000000..ff34ad2
--- /dev/null
+++ b/data/datalist
@@ -0,0 +1,3 @@
+specData
+speciesMap
+validTaxIds
diff --git a/data/specData.rda b/data/specData.rda
index 69b9848..13bf34a 100644
Binary files a/data/specData.rda and b/data/specData.rda differ
diff --git a/data/speciesMap.rda b/data/speciesMap.rda
index 86807c2..5ea91e3 100644
Binary files a/data/speciesMap.rda and b/data/speciesMap.rda differ
diff --git a/data/validTaxIds.rda b/data/validTaxIds.rda
index 5a2866b..94212cc 100644
Binary files a/data/validTaxIds.rda and b/data/validTaxIds.rda differ
diff --git a/inst/scripts/updateGenomeInfoDbData.R b/inst/scripts/updateGenomeInfoDbData.R
index 8cfcca8..d688958 100644
--- a/inst/scripts/updateGenomeInfoDbData.R
+++ b/inst/scripts/updateGenomeInfoDbData.R
@@ -19,8 +19,9 @@
species[[3]] <- gsub('\t','',species[[3]])
## throw away rows where the third column doesn't say 'scientific name'
keep <- grepl('scientific name', species[[3]])
- species <- species[keep,1:2]
-
+ keep2 <- grepl('synonym', species[[3]])
+ species <- species[(keep | keep2), 1:2]
+
## split second column by first space:
rawSpec <- species[[2]]
spltSpec <- strsplit(rawSpec, split=" ")
--
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