[med-svn] r17509 - in trunk/packages/R/r-bioc-variantannotation/trunk/debian: . patches tests
Andreas Tille
tille at moszumanska.debian.org
Thu Jul 24 07:44:33 UTC 2014
Author: tille
Date: 2014-07-24 07:44:33 +0000 (Thu, 24 Jul 2014)
New Revision: 17509
Modified:
trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test
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/tests/control
Log:
Remove another test since the according database is not available as Debian package; realise that we need to package r-bioc-snpstats to run the test suite
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test 2014-07-24 07:34:32 UTC (rev 17508)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test 2014-07-24 07:44:33 UTC (rev 17509)
@@ -30,4 +30,11 @@
original files from inst/unitTests to the installation directory or you
rebuild this package by deactivating the patch in the series file.
+
+ATTENTION: There will be one failed test until the package
+
+ r-bioc-snpstats
+
+will be available.
+
-- Andreas Tille <tille at debian.org> Thu, 24 Jul 2014 08:35:54 +0200
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2014-07-24 07:34:32 UTC (rev 17508)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2014-07-24 07:44:33 UTC (rev 17509)
@@ -29,6 +29,7 @@
r-bioc-iranges,
r-bioc-annotationdbi,
r-bioc-genomicfeatures (>= 1.15.15)
+Suggests: r-bioc-snpstats
Description: BioConductor annotation of genetic variants
This BioConductor package provides R functions to annotate variants,
compute amino acid coding changess and to predict coding outcomes.
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 2014-07-24 07:34:32 UTC (rev 17508)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2014-07-24 07:44:33 UTC (rev 17509)
@@ -1,7 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Thu, 24 Jul 2014 08:35:54 +0200
Description: Make test independent from TxDb.Hsapiens.UCSC.hg19.knownGene
- (see debian/README.test)
+ and other not packaged databases (see debian/README.test)
--- a/inst/unitTests/test_SIFTandPolyPhen.R
+++ /dev/null
@@ -199,3 +199,108 @@
- current <- locateVariants(q, txdb, PromoterVariants())
- checkIdentical(unique(current$GENEID), "79174")
-}
+--- a/inst/unitTests/test_predictCoding-methods.R
++++ /dev/null
+@@ -1,102 +0,0 @@
+-library(BSgenome.Hsapiens.UCSC.hg19)
+-fun <- VariantAnnotation:::.predictCodingGRangesList
+-cdsbytx <- GRangesList(tx1=GRanges(seqnames="chr1",
+- IRanges(c(10001, 10010), width=5),
+- strand="+"),
+- tx2=GRanges(seqnames="chr1",
+- IRanges(c(10100, 10001), width=5),
+- strand="-"),
+- tx3=GRanges(seqnames="chr1",
+- IRanges(c(10010, 10001), width=5),
+- strand="-"))
+-
+-test_predictCoding_empty <- function()
+-{
+- query <- GRanges("chr1", IRanges(start=c(1, 10, 20), width=1))
+- alt <- DNAStringSet(c("G", "T", "A"))
+- current <- fun(query, cdsbytx, Hsapiens, alt)
+- expected <- GRanges()
+- checkIdentical(current, expected)
+-}
+-
+-test_predictCoding_varAllele <- function()
+-{
+- variant=DNAStringSet(c("G", "", "C", "AA", "GGA"))
+- query <- GRanges(seqnames="chr1",
+- ranges=IRanges(c(rep(10003, 3), 10011, 10101),
+- width=c(1, 1, 1, 2, 3)),
+- strand=c("+", "-", "*", "*", "*"),
+- variant=variant)
+- names(query) <- LETTERS[1:5]
+- current <- suppressWarnings(fun(query, cdsbytx[1:2], Hsapiens, variant))
+-
+- current_varaa <- values(current[names(current) == "B"])[["VARAA"]]
+- checkTrue(as.character(current_varaa) == "")
+-
+- current_consequence <- values(current[names(current) == "B"])[["CONSEQUENCE"]]
+- checkTrue(current_consequence == "not translated")
+-
+- variant=DNAStringSet(c("GGA", "GGA"))
+- query <- GRanges("chr1", IRanges(rep(10101, 2), width=c(2,3)), variant=variant)
+- current <- suppressWarnings(fun(query, cdsbytx[1:2], Hsapiens, variant))
+- checkIdentical(as.character(mcols(current)$VARCODON), c("TAGGGG", "TTCCGG"))
+-
+- ## TODO : add test for codon width based on 1,2,3 position
+-}
+-
+-test_refLocsToLocalLocs <- function()
+-{
+- ## both in 'first' cds
+- query <- GRanges(seqnames="chr1",
+- ranges=IRanges(rep(c(10002, 10005), 2), width=1),
+- strand=c("+", "+", "-", "-"))
+- current <- refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)])
+- expected <- IRanges(c(2, 5, 9, 6), width=1)
+- checkIdentical(values(current)[["CDSLOC"]], expected)
+- expected <- c(1L, 2L, 3L, 2L)
+- checkIdentical(unlist(current$PROTEINLOC, use.names=FALSE), expected)
+-
+- ## one in each cds
+- query <- GRanges(seqnames="chr1",
+- ranges=IRanges(rep(c(10002, 10011), 2), width=1),
+- strand=c("+", "+", "-", "-"))
+- current <- refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)])
+- expected <- IRanges(c(2, 7, 9, 4), width=1)
+- checkIdentical(values(current)[["CDSLOC"]], expected)
+- expected <- c(1L, 3L, 3L, 2L)
+- checkIdentical(unlist(current$PROTEINLOC, use.names=FALSE), expected)
+-
+- ## both in 'last' cds
+- query <- GRanges(seqnames="chr1",
+- ranges=IRanges(rep(c(10010, 10013), 2), width=1),
+- strand=c("+", "+", "-", "-"))
+- current <- refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)])
+- 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)
+-}
+-
+-test_predictCoding_strand <- function()
+-{
+- variant=DNAStringSet(c("G", "G", "C", "T", "G"))
+- query <- GRanges(seqnames="chr1",
+- ranges=IRanges(c(rep(10003, 3), 10011, 10101), width=1),
+- strand=c("+", "-", "*", "*", "*"),
+- variant=variant)
+- names(query) <- LETTERS[1:5]
+- current <- suppressWarnings(fun(query, cdsbytx, Hsapiens, variant))
+-
+- expected <- c("G", "C", "C", "C", "G", "G", "T", "A", "C")
+- checkIdentical(as.character(values(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))
+-}
+-
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/control 2014-07-24 07:34:32 UTC (rev 17508)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/control 2014-07-24 07:44:33 UTC (rev 17509)
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, r-cran-runit
+Depends: @, r-cran-runit, r-bioc-snpstats
Restrictions: allow-stderr
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