[med-svn] r19419 - in trunk/packages/R/r-bioc-variantannotation/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Sun Jun 28 12:56:31 UTC 2015
Author: tille
Date: 2015-06-28 12:56:31 +0000 (Sun, 28 Jun 2015)
New Revision: 19419
Modified:
trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog
trunk/packages/R/r-bioc-variantannotation/trunk/debian/control
trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch
trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
New upstream version
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog 2015-06-28 06:29:00 UTC (rev 19418)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog 2015-06-28 12:56:31 UTC (rev 19419)
@@ -1,3 +1,9 @@
+r-bioc-variantannotation (1.14.4-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Sun, 28 Jun 2015 14:34:18 +0200
+
r-bioc-variantannotation (1.12.0-1) experimental; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2015-06-28 06:29:00 UTC (rev 19418)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2015-06-28 12:56:31 UTC (rev 19419)
@@ -2,13 +2,12 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: gnu-r
-Testsuite: autopkgtest
Priority: optional
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
- r-bioc-genomicfeatures (>= 1.18.0),
- r-bioc-bsgenome (>= 1.34.0)
+ r-bioc-genomicfeatures (>= 1.20.1),
+ r-bioc-bsgenome (>= 1.36.1)
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-variantannotation/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-variantannotation/trunk/
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2015-06-28 06:29:00 UTC (rev 19418)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2015-06-28 12:56:31 UTC (rev 19419)
@@ -66,10 +66,10 @@
-
--- a/inst/unitTests/test_locateVariants-methods.R
+++ /dev/null
-@@ -1,132 +0,0 @@
+@@ -1,136 +0,0 @@
-library(TxDb.Hsapiens.UCSC.hg19.knownGene)
-txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
--cdsbytx <- cdsBy(txdb)
+-cdsbytx <- cdsBy(txdb, use.names=TRUE)
-intbytx <- intronsByTranscript(txdb)
-txbygene <- transcriptsBy(txdb, "gene")
-
@@ -78,27 +78,7 @@
- 18209442, 18121652, 24314750, 25508661),
- width=c(1,1,1,1,3,3,2,2)),
- strand=c("-", "-", "-", "+", "+", "+", "+", "+"))
--
--test_locateVariants_subject <- function()
--{
-- cols <- c("LOCATION", "QUERYID", "TXID", "CDSID")
-- loc1 <- locateVariants(gr, txdb, CodingVariants())
-- loc2 <- locateVariants(gr, cdsbytx, CodingVariants())
-- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
--
-- loc1 <- locateVariants(gr, txdb, IntronVariants())
-- loc2 <- locateVariants(gr, intbytx, IntronVariants())
-- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
-
-- loc1 <- locateVariants(gr, txdb, SpliceSiteVariants())
-- loc2 <- locateVariants(gr, intbytx, SpliceSiteVariants())
-- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
--
-- loc1 <- locateVariants(gr, txdb, IntergenicVariants())
-- loc2 <- locateVariants(gr, txbygene, IntergenicVariants())
-- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
--}
--
-test_locateVariants_upstream_downstream <- function()
-{
- loc <- locateVariants(gr, txdb, IntergenicVariants(1, 1))
@@ -122,12 +102,13 @@
- vcf <- readVcf(fl, "hg19")
- vcf <- renameSeqlevels(vcf, c("1" = "chr1"))
- loc1 <- locateVariants(vcf, txdb, IntergenicVariants())
-- loc2 <- locateVariants(rowData(vcf), txdb, IntergenicVariants())
+- loc2 <- locateVariants(rowRanges(vcf), txdb, IntergenicVariants())
- checkIdentical(loc1, loc2)
-}
-
-test_locateVariants_ignore.strand <- function()
-{
+- cdsbytx <- cdsbytx[1:5]
- gr <- GRanges("chr1", IRanges(c(12190, 12595, 13403), width=1), "-")
- loc1 <- locateVariants(gr, cdsbytx, CodingVariants(),
- ignore.strand=TRUE)
@@ -199,9 +180,33 @@
- current <- locateVariants(q, txdb, PromoterVariants())
- checkIdentical(unique(current$GENEID), "79174")
-}
+-
+-test_locateVariants_match_predictCoding <- function()
+-{
+- library(BSgenome.Hsapiens.UCSC.hg19)
+- gr <- GRanges("chr20", IRanges(
+- start=c(77055, 77054, 77054, 77058, 77057, 77057, 77055),
+- end=c(77055, 77055, 77055, 77058, 77058, 77058, 77054)),
+- paramRangeID=rep(NA, 7))
+- fixed <- DataFrame(
+- REF=DNAStringSet(c('T', 'AT', 'AT', 'A', 'AA', 'AA', 'T')),
+- ALT=DNAStringSetList('G', 'A', 'ATT', 'G', 'A', 'AAT', 'G'),
+- QUAL=70, FILTER="PASS")
+- vcf <- VCF(rowRanges=gr, fixed=fixed)
+-
+- ## coding regions match, zero-width
+- loc <- locateVariants(vcf, txdb, CodingVariants())
+- coding <- predictCoding(vcf, txdb, Hsapiens)
+- checkIdentical(loc$QUERYID, as.integer(1:7))
+- checkIdentical(length(coding) , 6L)
+- checkIdentical(loc$CDSID[1:6], coding$CDSID)
+- checkIdentical(as.character(coding$VARCODON[c(1,4)]),
+- as.character(DNAStringSet(c("AAG", "TAG"))))
+-}
--- a/inst/unitTests/test_predictCoding-methods.R
+++ /dev/null
-@@ -1,102 +0,0 @@
+@@ -1,110 +0,0 @@
+-quiet <- suppressWarnings
-library(BSgenome.Hsapiens.UCSC.hg19)
-fun <- VariantAnnotation:::.predictCodingGRangesList
-cdsbytx <- GRangesList(tx1=GRanges(seqnames="chr1",
@@ -217,8 +222,7 @@
-test_predictCoding_empty <- function()
-{
- query <- GRanges("chr1", IRanges(start=c(1, 10, 20), width=1))
-- alt <- DNAStringSet(c("G", "T", "A"))
-- current <- fun(query, cdsbytx, Hsapiens, alt)
+- current <- fun(query, cdsbytx, Hsapiens, DNAStringSet(c("G", "T", "A")))
- checkIdentical(dim(mcols(current)), c(0L, 8L))
-}
-
@@ -231,54 +235,47 @@
- strand=c("+", "-", "*", "*", "*"),
- variant=variant)
- names(query) <- LETTERS[1:5]
-- current <- suppressWarnings(fun(query, cdsbytx[1:2], Hsapiens, variant))
+- current <- quiet(fun(query, cdsbytx[1:2], Hsapiens, variant))
-
- current_varaa <- values(current[names(current) == "B"])[["VARAA"]]
- checkTrue(as.character(current_varaa) == "")
-
-- current_consequence <- values(current[names(current) == "B"])[["CONSEQUENCE"]]
+- current_consequence <-
+- values(current[names(current) == "B"])[["CONSEQUENCE"]]
- checkTrue(current_consequence == "not translated")
-
- variant=DNAStringSet(c("GGA", "GGA"))
-- query <- GRanges("chr1", IRanges(rep(10101, 2), width=c(2,3)), variant=variant)
-- current <- suppressWarnings(fun(query, cdsbytx[1:2], Hsapiens, variant))
-- checkIdentical(as.character(mcols(current)$VARCODON), c("TAGGGG", "TTCCGG"))
--
-- ## TODO : add test for codon width based on 1,2,3 position
+- query <- GRanges("chr1", IRanges(rep(10101, 2), width=c(2,3)),
+- variant=variant)
+- current <- quiet(fun(query, cdsbytx[1:2], Hsapiens, variant))
+- checkIdentical(as.character(mcols(current)$VARCODON), c("", "TTCCGG"))
-}
-
--test_refLocsToLocalLocs <- function()
+-test_mapToTranscripts <- function()
-{
-- quiet <- suppressWarnings
- ## both in 'first' cds
- query <- GRanges(seqnames="chr1",
- ranges=IRanges(rep(c(10002, 10005), 2), width=1),
- strand=c("+", "+", "-", "-"))
-- current <- quiet(refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)]))
+- current <- mapToTranscripts(query, cdsbytx[c(1,3)], ignore.strand=FALSE)
- expected <- IRanges(c(2, 5, 9, 6), width=1)
-- checkIdentical(values(current)[["CDSLOC"]], expected)
-- expected <- c(1L, 2L, 3L, 2L)
-- checkIdentical(unlist(current$PROTEINLOC, use.names=FALSE), expected)
+- checkIdentical(ranges(current), expected)
-
- ## one in each cds
- query <- GRanges(seqnames="chr1",
- ranges=IRanges(rep(c(10002, 10011), 2), width=1),
- strand=c("+", "+", "-", "-"))
-- current <- quiet(refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)]))
+- current <- mapToTranscripts(query, cdsbytx[c(1,3)], ignore.strand=FALSE)
- expected <- IRanges(c(2, 7, 9, 4), width=1)
-- checkIdentical(values(current)[["CDSLOC"]], expected)
-- expected <- c(1L, 3L, 3L, 2L)
-- checkIdentical(unlist(current$PROTEINLOC, use.names=FALSE), expected)
+- checkIdentical(ranges(current), expected)
-
- ## both in 'last' cds
- query <- GRanges(seqnames="chr1",
- ranges=IRanges(rep(c(10010, 10013), 2), width=1),
- strand=c("+", "+", "-", "-"))
-- current <- quiet(refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)]))
+- current <- mapToTranscripts(query, cdsbytx[c(1,3)], ignore.strand=FALSE)
- expected <- IRanges(c(6, 9, 5, 2), width=1)
-- checkIdentical(values(current)[["CDSLOC"]], expected)
-- expected <- c(2L, 3L, 2L, 1L)
-- checkIdentical(unlist(current$PROTEINLOC, use.names=FALSE), expected)
+- checkIdentical(ranges(current), expected)
-}
-
-test_predictCoding_strand <- function()
@@ -289,18 +286,33 @@
- strand=c("+", "-", "*", "*", "*"),
- variant=variant)
- names(query) <- LETTERS[1:5]
-- current <- suppressWarnings(fun(query, cdsbytx, Hsapiens, variant))
-
+- current <- quiet(fun(query, cdsbytx, Hsapiens, variant))
- expected <- c("G", "C", "C", "C", "G", "G", "T", "A", "C")
- checkIdentical(as.character(mcols(current)$varAllele), expected)
-
-- ## ignore.strand
-- strand(query) <- "+"
-- p1 <- suppressWarnings(fun(query, cdsbytx, Hsapiens, variant,
-- ignore.strand=TRUE))
-- checkIdentical(12L, length(p1))
-- p2 <- suppressWarnings(fun(query, cdsbytx, Hsapiens, variant,
-- ignore.strand=FALSE))
-- checkIdentical(4L, length(p2))
+- ## query "+", subject "-"
+- v <- variant[2]
+- q <- query[2]
+- strand(q) <- "+"
+- s <- cdsbytx[3]
+- current <- quiet(fun(q, s, Hsapiens, v, ignore.strand=FALSE))
+- checkIdentical(length(current), 0L)
+-
+- current <- quiet(fun(q, s, Hsapiens, v, ignore.strand=TRUE))
+- checkIdentical(as.character(mcols(current)$REFAA), "V")
+- checkIdentical(as.character(mcols(current)$VARAA), "A")
+- checkIdentical(mcols(current)$CDSLOC, IRanges(8, 8))
+-
+- ## query "-", subject "+"
+- strand(q) <- "-"
+- s <- cdsbytx[1]
+- current <- quiet(fun(q, s, Hsapiens, v, ignore.strand=FALSE))
+- checkIdentical(length(current), 0L)
+-
+- current <- quiet(fun(q, s, Hsapiens, v, ignore.strand=TRUE))
+- checkIdentical(as.character(mcols(current)$REFAA), "*")
+- checkIdentical(as.character(mcols(current)$VARAA), "*")
+- checkIdentical(mcols(current)$CDSLOC, IRanges(3, 3))
-}
-
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-06-28 06:29:00 UTC (rev 19418)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-06-28 12:56:31 UTC (rev 19419)
@@ -8,12 +8,12 @@
@@ -12,7 +12,7 @@ Authors at R: c(person("Valerie", "Obenchai
License: Artistic-2.0
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.7.7), GenomeInfoDb
- (>= 1.1.3), GenomicRanges (>= 1.17.40), Rsamtools (>= 1.17.26)
--Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.2.3), IRanges
-+Imports: utils, DBI, Biobase, S4Vectors (>= 0.2.3), IRanges
- (>= 1.99.28), XVector (>= 0.5.6), Biostrings (>= 2.33.5),
+ (>= 1.1.3), GenomicRanges (>= 1.19.47), Rsamtools (>= 1.19.52)
+-Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.5.14), IRanges
++Imports: utils, DBI, Biobase, S4Vectors (>= 0.5.14), IRanges
+ (>= 2.1.27), XVector (>= 0.5.6), Biostrings (>= 2.33.5),
AnnotationDbi (>= 1.27.9), BSgenome, rtracklayer (>= 1.25.16),
- GenomicFeatures (>= 1.17.13)
+ GenomicFeatures (>= 1.19.17)
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,8 +12,6 @@ import(GenomicRanges)
More information about the debian-med-commit
mailing list