Complete test for R functions

.gitignore

@@ -27,3 +27,4 @@ dist
 **/env-*
 **/*.log
 **/*.test
+**/vknr.test

python/test/test_rsidvar.py

@@ -125,7 +125,7 @@ def test_find_vr_chrompos_range(self):
         self.assertEqual(xlast, 8)
 
     def test_find_vr_chrompos_range_notfound(self):
-        xrsid, xfirst, xlast = bs.find_vr_chrompos_range(vrsrc, 0, 9, 0xfffffff0, 0xffffff00, 0xfffffff0)
+        xrsid, xfirst, xlast = bs.find_vr_chrompos_range(vrsrc, 0, 9, 0xff, 0xffffff00, 0xfffffff0)
         self.assertEqual(xrsid, 0)
         self.assertEqual(xfirst, 10)
         self.assertEqual(xlast, 9)

r/variantkey/tests/testthat/test-binsearch.R

@@ -14,6 +14,6 @@ test_that("MmapBinfile", {
 })
 
 test_that("MunmapBinfile", {
-    err <- MunmapBinfile(mm$SRC,mm$FD, mm$SIZE)
+    err <- MunmapBinfile(mm$SRC, mm$FD, mm$SIZE)
     expect_that(err, equals(0))
 })

r/variantkey/tests/testthat/test-nrvk.R

@@ -8,12 +8,51 @@ library(variantkey)
 # @license    MIT (see LICENSE)
 # @link       https://github.com/genomicsplc/variantkey
 
+x <- rbind(
+    list("0800c35093ace339",  "1", 100001, 0x00000004, 0x01, 0x01, "N", "A"),
+    list("1000c3517f91cdb1",  "2", 100002, 0x0000000e, 0x0b, 0x01, "AAGAAAGAAAG", "A"),
+    list("1800c351f61f65d3",  "3", 100003, 0x0000000e, 0x01, 0x0b, "A", "AAGAAAGAAAG"),
+    list("2000c3521f1c15ab",  "4", 100004, 0x0000000e, 0x08, 0x04, "ACGTACGT", "ACGT"),
+    list("2800c352d8f2d5b5",  "5", 100005, 0x0000000e, 0x04, 0x08, "ACGT", "ACGTACGT"),
+    list("5000c3553bbf9c19", "10", 100010, 0x00000012, 0x08, 0x08, "ACGTACGT", "CGTACGTA"),
+    list("b000c35b64690b25", "22", 100022, 0x0000000b, 0x08, 0x01, "ACGTACGT", "N"),
+    list("b800c35bbcece603",  "X", 100023, 0x0000000e, 0x0a, 0x02, "AAAAAAAAGG", "AG"),
+    list("c000c35c63741ee7",  "Y", 100024, 0x0000000e, 0x02, 0x0a, "AG", "AAAAAAAAGG"),
+    list("c800c35c96c18499", "MT", 100025, 0x00000012, 0x04, 0x0c, "ACGT", "AAACCCGGGTTT")
+)
+colnames(x) <- list("vk", "chrom", "pos", "ralen", "sizeref", "sizealt", "ref", "alt")
+
 test_that("MmapBinfile", {
     vknr <<- MmapBinfile("../../../../c/test/data/vknr.10.bin")
     expect_that(vknr$SIZE, equals(299))
 })
 
+test_that("FindRefAltByVariantkey", {
+    res <- mapply(FindRefAltByVariantkey, vk = unlist(x[,"vk"]), MoreArgs = list(src = vknr$SRC, last = vknr$LAST), SIMPLIFY = TRUE, USE.NAMES = FALSE)
+    expect_that(unlist(res[1,]), equals(unlist(x[,"ref"])))
+    expect_that(unlist(res[2,]), equals(unlist(x[,"alt"])))
+    expect_that(unlist(res[3,]), equals(unlist(x[,"sizeref"])))
+    expect_that(unlist(res[4,]), equals(unlist(x[,"sizealt"])))
+    expect_that(unlist(res[5,]), equals(unlist(x[,"ralen"]) - 2))
+})
+
+test_that("ReverseVariantkey", {
+    res <- mapply(ReverseVariantkey, vk = unlist(x[,"vk"]), MoreArgs = list(src = vknr$SRC, last = vknr$LAST), SIMPLIFY = TRUE, USE.NAMES = FALSE)
+    expect_that(unlist(res[1,]), equals(unlist(x[,"chrom"])))
+    expect_that(unlist(res[2,]), equals(unlist(x[,"pos"])))
+    expect_that(unlist(res[3,]), equals(unlist(x[,"ref"])))
+    expect_that(unlist(res[4,]), equals(unlist(x[,"alt"])))
+    expect_that(unlist(res[5,]), equals(unlist(x[,"sizeref"])))
+    expect_that(unlist(res[6,]), equals(unlist(x[,"sizealt"])))
+    expect_that(unlist(res[7,]), equals(unlist(x[,"ralen"]) - 2))
+})
+
+test_that("VknrBinToTsv", {
+    size <- VknrBinToTsv(vknr$SRC, vknr$LAST, "vknr.test")
+    expect_that(size, equals(305))
+})
+
 test_that("MunmapBinfile", {
-    err <- MunmapBinfile(vknr$SRC,vknr$FD, vknr$SIZE)
+    err <- MunmapBinfile(vknr$SRC, vknr$FD, vknr$SIZE)
     expect_that(err, equals(0))
 })

r/variantkey/tests/testthat/test-rsidvar.R

@@ -8,6 +8,20 @@ library(variantkey)
 # @license    MIT (see LICENSE)
 # @link       https://github.com/genomicsplc/variantkey
 
+x <- rbind(
+    list(0, 0x00000001, "08027a2580338000", 0x01, 0x0004F44B, 0x00338000),
+    list(1, 0x00000007, "4800a1fe439e3918", 0x09, 0x000143FC, 0x439E3918),
+    list(2, 0x0000000B, "4800a1fe7555eb16", 0x09, 0x000143FC, 0x7555EB16),
+    list(3, 0x00000061, "80010274003a0000", 0x10, 0x000204E8, 0x003A0000),
+    list(4, 0x00000065, "8001028d00138000", 0x10, 0x0002051A, 0x00138000),
+    list(5, 0x000003E5, "80010299007a0000", 0x10, 0x00020532, 0x007A0000),
+    list(6, 0x000003F1, "a0012b62003a0000", 0x14, 0x000256C4, 0x003A0000),
+    list(7, 0x000026F5, "a0012b6280708000", 0x14, 0x000256C5, 0x00708000),
+    list(8, 0x000186A3, "a0012b65e3256692", 0x14, 0x000256CB, 0x63256692),
+    list(9, 0x00019919, "a0012b67d5439803", 0x14, 0x000256CF, 0x55439803)
+)
+colnames(x) <- list("item", "rsid", "vk", "chrom", "pos", "refalt")
+
 test_that("MmapBinfile", {
     rsvk <<- MmapBinfile("../../../../c/test/data/rsvk.10.bin")
     expect_that(rsvk$SIZE, equals(120))
@@ -17,11 +31,82 @@ test_that("MmapBinfile", {
     expect_that(rsvk$SIZE, equals(120))
 })
 
+test_that("GetVrRsid", {
+    res <- mapply(GetVrRsid, item = unlist(x[,"item"]), MoreArgs = list(src = vkrs$SRC), SIMPLIFY = TRUE, USE.NAMES = FALSE)
+    expect_that(res, equals(unlist(x[,"rsid"])))
+})
+
+test_that("GetRvVariantkey", {
+    res <- mapply(GetRvVariantkey, item = unlist(x[,"item"]), MoreArgs = list(src = rsvk$SRC), SIMPLIFY = TRUE, USE.NAMES = FALSE)
+    expect_that(res, equals(unlist(x[,"vk"])))
+})
+
+test_that("FindRvVariantkeyByRsid", {
+    res <- mapply(FindRvVariantkeyByRsid, rsid = unlist(x[,"rsid"]), MoreArgs = list(src = rsvk$SRC, first = 0, last = 9), SIMPLIFY = TRUE, USE.NAMES = FALSE)
+    expect_that(unlist(res[1,]), equals(unlist(x[,"vk"])))
+    expect_that(unlist(res[2,]), equals(unlist(x[,"item"])))
+})
+
+test_that("FindRvVariantkeyByRsidNotFound", {
+    res <- FindRvVariantkeyByRsid(rsvk$SRC, 0, 9, 0xfffffff0)
+    expect_that(res$VK, equals("0000000000000000"))
+    expect_that(res$FIRST, equals(10))
+})
+
+test_that("GetNextRvVariantkeyByRsid", {
+    res <- GetNextRvVariantkeyByRsid(rsvk$SRC, 2, 9, 0x00000061)
+    expect_that(res$VK, equals("80010274003a0000"))
+    expect_that(res$POS, equals(3))
+    res <- GetNextRvVariantkeyByRsid(rsvk$SRC, res$POS, 9, 0x00000061)
+    expect_that(res$VK, equals("0000000000000000"))
+    expect_that(res$POS, equals(4))
+})
+
+test_that("FindVrRsidByVariantkey", {
+    res <- mapply(FindVrRsidByVariantkey, vk = unlist(x[,"vk"]), MoreArgs = list(src = vkrs$SRC, first = 0, last = 9), SIMPLIFY = TRUE, USE.NAMES = FALSE)
+    expect_that(unlist(res[1,]), equals(unlist(x[,"rsid"])))
+    expect_that(unlist(res[2,]), equals(unlist(x[,"item"])))
+})
+
+test_that("FindVrRsidByVariantkeyNotFound", {
+    res <- FindVrRsidByVariantkey(vkrs$SRC, 0, 9, "fffffffffffffff0")
+    expect_that(res$RSID, equals(0))
+    expect_that(res$FIRST, equals(10))
+})
+
+test_that("FindVrChromposRange", {
+    res <- FindVrChromposRange(vkrs$SRC, 0, 9, 0x14, 0x000256C5, 0x000256CB)
+    expect_that(res$RSID, equals(0x000026F5))
+    expect_that(res$FIRST, equals(7))
+    expect_that(res$LAST, equals(8))
+})
+
+test_that("FindVrChromposRangeNotFound", {
+    res <- FindVrChromposRange(vkrs$SRC, 0, 9, 0xff, 0xffffff00, 0xfffffff0)
+    expect_that(res$RSID, equals(0))
+    expect_that(res$FIRST, equals(10))
+    expect_that(res$LAST, equals(9))
+})
+
+
+#    def test_find_all_rv_variantkey_by_rsid(self):
+#        vks = bs.find_all_rv_variantkey_by_rsid(rvmsrc, 0, 9, 0x00000003)
+#        self.assertEqual(len(vks), 3)
+#        self.assertEqual(vks[0], 0x80010274003A0000)
+#        self.assertEqual(vks[1], 0x8001028D00138000)
+#        self.assertEqual(vks[2], 0x80010299007A0000)
+
+
+#    def test_find_all_rv_variantkey_by_rsid_notfound(self):
+#        vks = bs.find_all_rv_variantkey_by_rsid(rvmsrc, 0, 9, 0xfffffff0)
+#        self.assertEqual(len(vks), 0)
+
+
 test_that("MunmapBinfile", {
-    err <- MunmapBinfile(rsvk$SRC,rsvk$FD, rsvk$SIZE)
+    err <- MunmapBinfile(rsvk$SRC, rsvk$FD, rsvk$SIZE)
     expect_that(err, equals(0))
-    err <- MunmapBinfile(rsvkm$SRC,rsvkm$FD, rsvkm$SIZE)
+    err <- MunmapBinfile(rsvkm$SRC, rsvkm$FD, rsvkm$SIZE)
     expect_that(err, equals(0))
-    err <- MunmapBinfile(vkrs$SRC,vkrs$FD, vkrs$SIZE)
+    err <- MunmapBinfile(vkrs$SRC, vkrs$FD, vkrs$SIZE)
     expect_that(err, equals(0))
 })