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Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 08 Jul 2014 10:55:48 +0200
Description: Skip test requiring pasillaBamSubset
This package contains a test suite which depends from a dataset provided at
http://bioconductor.org/packages/release/data/experiment/html/pasillaBamSubset.html
which is not packaged for Debian.
See README.test for more information.
--- a/inst/unitTests/test_readGAlignmentsList.R
+++ /dev/null
@@ -1,184 +0,0 @@
-library(pasillaBamSubset)
-chr4 <- untreated3_chr4()
-
-test_readGAlignmentsList_construction <- function()
-{
- fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
- bf <- BamFile(fl, asMates=TRUE)
- galist <- readGAlignmentsList(fl)
- checkTrue(is.null(names(galist)))
- galist <- readGAlignmentsList(fl, use.names=TRUE)
- target <- c("EAS54_61:4:143:69:578", "EAS219_FC30151:7:51:1429:1043")
- checkIdentical(names(galist)[1:2], target)
-
- ## first segment first
- param <- ScanBamParam(what="flag")
- galist <- readGAlignmentsList(fl, param=param)
- mates <- galist[mcols(galist)$mate_status == "mated"]
- flagBit <- bamFlagAsBitMatrix(mcols(unlist(mates))$flag,
- bitnames="isFirstMateRead")
- m <- matrix(flagBit, nrow=2)
- checkIdentical(c(1572L, 0), rowSums(m))
-}
-
-test_readGAlignmentsList_noYieldSize <- function()
-{
- fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
- bf <- BamFile(fl, asMates=TRUE)
- galist <- readGAlignmentsList(fl)
- checkTrue(validObject(galist))
-}
-
-test_readGAlignmentsList_yieldSize <- function()
-{
- bf <- BamFile(chr4, asMates=TRUE, yieldSize=1)
- scn1 <- scanBam(bf)
- galist1 <- readGAlignmentsList(bf)
- checkTrue(length(scn1[[1]]$qname) == 2)
- checkTrue(length(unique(scn1[[1]]$qname)) == 1)
- checkTrue(length(unique(scn1[[1]]$qname)) == length(galist1))
-
- bf <- BamFile(chr4, asMates=TRUE, yieldSize=2)
- scn2 <- scanBam(bf)
- galist2 <- readGAlignmentsList(bf)
- checkTrue(length(scn2[[1]]$qname) == 4)
- checkTrue(length(unique(scn2[[1]]$qname)) == 2)
- checkTrue(length(unique(scn2[[1]]$qname)) == length(galist2))
-}
-
-test_readGAlignmentsList_mcols <- function()
-{
- bf <- BamFile(chr4, asMates=TRUE, yieldSize=100)
- param <- ScanBamParam(tag=("NM"))
- galist <- readGAlignmentsList(bf, param=param)
- checkIdentical(colnames(mcols(unlist(galist))), "NM")
- checkTrue(names(mcols(galist)) == "mate_status")
-
- param <- ScanBamParam(tag=("FO"))
- galist <- readGAlignmentsList(bf, param=param)
- checkIdentical(rep.int(NA, length(unlist(galist))),
- mcols(unlist(galist))[["FO"]])
-}
-
-test_readGAlignmentsList_compare_pairs <- function()
-{
- bamfile <- BamFile(untreated3_chr4(), asMates=TRUE)
- galist <- readGAlignmentsList(bamfile)
- mates <- galist[mcols(galist)$mate_status == "mated"]
- galp <- readGAlignmentPairs(bamfile)
- checkIdentical(length(galp), 75409L)
- tbl <- table(mcols(galist))
- checkIdentical(tbl[["mated"]], 75409L)
- checkIdentical(tbl[["ambiguous"]], 0L)
- checkIdentical(tbl[["unmated"]], 21227L)
-}
-
-test_readGAlignmentsList_flags <- function()
-{
- bamfile <- BamFile(untreated3_chr4(), asMates=TRUE)
- param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
- galist <- readGAlignmentsList(bamfile, param=param)
- status <- table(mcols(galist)$mate_status)
- checkIdentical(status[["mated"]], 45828L)
- checkIdentical(status[["ambiguous"]], 0L)
- checkIdentical(status[["unmated"]], 0L)
-}
-
-## toy_bamfile read summary:
-## --------------------------
-
-## single-end
-## s001: 1 primary alignment
-## s002: 1 primary alignment + 3 secondary alignments
-## s003: unmapped
-
-## paired-end
-## p991: 1 pair with a missing mate (can happen if file was subsetted)
-## p992: 1 pair with 1st mate unmapped and 2nd mate mapped
-## p993: 1 pair with both mates unmapped
-
-## multi-segments
-## m001: 3 segments in the template (index of each segment is known)
-## m002: 3 segments in the template (index of each segment was lost)
-
-## mapped pairs ('pi' tag only exists for these mapped pairs)
-## p001: 1 primary proper pair
-## p002: 1 primary non proper pair
-## p003: 2 proper pairs: 1 primary + 1 secondary
-## p004: 2 non proper pairs: 1 primary + 1 secondary
-## p005: 2 primary pairs
-## p006: 3 pairs: 1 primary proper + 1 secondary proper +
-## 1 secondary non proper
-## p007: 2 pairs mapped to the same position:
-## 1 primary proper + 1 secondary proper
-## p008: 3 pairs mapped to the same position: 1 primary proper +
-## 1 secondary proper + 1 secondary non proper
-## p009: 3 pairs mapped to the same position:
-## 1 primary proper + 2 secondary proper.
-source(system.file("unitTests", "test_readGAlignmentPairs.R",
- package="GenomicAlignments"))
-bf <- BamFile(toy_bamfile, asMates=TRUE)
-
-test_readGAlignmentsList_toybamfile <- function()
-{
- param <- ScanBamParam(tag="pi")
- galp <- readGAlignmentPairs(toy_bamfile, use.names=TRUE, param=param)
- galist <- readGAlignmentsList(bf, use.names=TRUE, param=param)
-
- ## 'mated'
- mated_galist <- unlist(galist[mcols(galist)$mate_status == "mated"])
- pi_target <- c("p001", "p002", "p003a", "p003b", "p004a", "p004b",
- "p005a", "p005b", "p006a", "p006b", "p006c",
- "p007a", "p007b", "p008a", "p008b", "p008c", "p009a")
- checkTrue(all(mcols(mated_galist)$pi %in% pi_target))
-
- ## 'ambiguous' GAList match 'dumped' GAPairs
- ambig_galist <- unlist(galist[mcols(galist)$mate_status == "ambiguous"])
- dumped_galp <- getDumpedAlignments()
- pi_target <- rep(c("p009b", "p009c"), each=2)
- checkIdentical(pi_target, sort(mcols(dumped_galp)$pi))
- checkIdentical(pi_target, sort(mcols(ambig_galist)$pi))
-
- ## 'unmated':
- unmated_galist <- unlist(galist[mcols(galist)$mate_status == "unmated"])
- ## unmated single-end, paired-end or multi-segment (no pi tags)
- name_target <- c("m001", "m002", "p991", "p992", "s001", "s002")
- unmated <- names(unmated_galist)[is.na(mcols(unmated_galist)$pi)]
- checkTrue(all(unmated %in% name_target))
- ## non-proper mapped-pairs (have pi tags)
- pi_target <- c("p002", "p004a", "p004b", "p006c", "p008c")
- unmated <- na.omit(unique(mcols(unmated_galist)$pi))
- checkTrue(all(unmated %in% pi_target))
-
- ## Reads of this type cannot be filtered out wrt readGAlignmentsList.
- ## They are always returned by readGAlignmentsList but never returned by
- ## readGAlignmentPairs.
- bamFlag(param) <- scanBamFlag(isProperPair=TRUE,
- hasUnmappedMate=FALSE,
- isUnmappedQuery=FALSE,
- isPaired=TRUE)
- galist <- readGAlignmentsList(bf, use.names=TRUE, param=param)
- unmated_galist <- unlist(galist[mcols(galist)$mate_status == "unmated"])
- unmated <- names(unmated_galist)[is.na(mcols(unmated_galist)$pi)]
- name_target <- c("m001", "m002", "p991")
- checkTrue(all(unmated %in% name_target))
-}
-
-test_readGAlignmentsList_which <- function()
-{
- ## 4 non-overlapping regions of interest: first two regions only overlap
- ## with first p001 mate and last two regions only with last p001 mate.
- my_ROI <- GRanges("chr2", IRanges(c(10, 15, 110, 115), width=1))
- my_ROI_labels <- c("chr2:10-10", "chr2:15-15",
- "chr2:110-110", "chr2:115-115")
- param <- ScanBamParam(tag="pi", which=my_ROI[c(1, 4)])
- target1 <- readGAlignmentsList(toy_bamfile, use.names=TRUE,
- param=param, with.which_label=TRUE)
- ## Duplicate results with distinct 'which_label'
- checkIdentical(2L, length(target1))
- checkIdentical(as.vector(mcols(target1)$mate_status), c("mated", "mated"))
- rng1 <- as.vector(mcols(unlist(target1[1]))$which_label)
- checkTrue(all(rng1 %in% my_ROI_labels[1]))
- rng2 <- as.vector(mcols(unlist(target1[2]))$which_label)
- checkTrue(all(rng2 %in% my_ROI_labels[4]))
-}
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