tests/testthat/test_bambi_ops.R
In mskilab/bambi: R to query barcode indices on bam files
library(testthat)
library(bambi)
library(bamUtils)
library(gUtils)
example_bam = 'subset_HCC1143_phased_possorted000005.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_bai = 'subset_HCC1143_phased_possorted000005.bam.bai'
example_lmdb = 'subset_HCC1143_phased_possorted000005_lmdb'
## in Ensembl format, e.g. 5
example_bam_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.bam'
example_bai_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.bam.bai'
example_lmdb_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle_lmdb'
example_CB_bam = 'subset_pbmc8k_possorted_genome_bam000025.CB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_CB_bai = 'subset_pbmc8k_possorted_genome_bam000025.CB.bam.bai'
example_CB_lmdb = 'subset_pbmc8k_possorted_genome_bam000025.CB_lmdb'
## in UCSC format, e.g. 5
example_CB_bam_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_CB_bai_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB.bam.bai'
example_CB_lmdb_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB_lmdb'
example_UB_bam = 'subset_pbmc8k_possorted_genome_bam000025.UB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_UB_bai = 'subset_pbmc8k_possorted_genome_bam000025.UB.bam.bai'
example_UB_lmdb = 'subset_pbmc8k_possorted_genome_bam000025.UB_lmdb'
## in UCSC format, e.g. 5
example_UB_bam_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_UB_bai_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB.bam.bai'
example_UB_lmdb_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB_lmd'
example_PS_bam = 'subset_HCC1143_phased_possorted000005.PS.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_PS_bai = 'subset_HCC1143_phased_possorted000005.PS.bam.bai'
example_PS_lmdb = 'subset_HCC1143_phased_possorted000005.PS_lmdb'
## in Ensembl format, e.g. chr5
example_PS_bam_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.PS.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_PS_bai_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.PS.bam.bai'
example_PS_lmdb_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.PS_lmdb'
bam_no_lmdb = 'bam_with_no_lmdb.bam'
######## R6_class.R
test_that('bambi class constructor', {
## Error in .subset2(public_bind_env, "initialize")(...) :
## BAM file not found. A valid BAM for 'bam_file' must be provided.
expect_error(bambi$new(bam_file = 'foobar'))
## Error in .subset2(public_bind_env, "initialize")(...) :
## Cannot open BAM. A valid BAM for 'bam_file' must be provided.
expect_error(bambi$new(bam_file = 'fake_bam.txt'))
## if (is.null(bamdb_path))
## Error in .subset2(public_bind_env, "initialize")(...) :
## Error: Pathname to bamdb LMDB subdirectory must be provided
expect_error(bambi$new(bam_file ='bam_with_no_lmdb.bam'))
## valid
foo = bambi$new(bam_file = example_bam)
expect_match(foo$bam_file, 'subset_HCC1143_phased_possorted000005.bam')
expect_match(foo$bamdb_path, 'subset_HCC1143_phased_possorted000005_lmdb')
})
test_that('bambi test method grab_bx()', {
## check works
foo = bambi$new(bam_file = example_bam)
## Error in foo$grab_cb() :
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo$grab_cb())
## UB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo$grab_ub())
###
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[1], 97)
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[2], 145)
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$mapq[1], 60)
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$mapq[2], 60)
expect_match(foo$grab_bx('CGGCTAGGTAGAATAC-1')$cigar[1], "80M47S")
expect_match(foo$grab_bx('CGGCTAGGTAGAATAC-1')$cigar[2], "37S113M")
expect_equal(length(foo$grab_bx('CGGCTAGGTAGAATAC-1')), 2)
expect_equal(length(foo$grab_bx('CGGCTAGGTAGAATAC-1', data.table=TRUE)), 22)
##
## if ((is.null(barcodes)) & (is.null(query))){
expect_equal(foo$grab_bx(), GRanges())
expect_equal(foo$grab_bx(data.table=TRUE), data.table())
##
## if ((!is.null(barcodes)) & (!is.null(query))){
## Error in foo$grab_bx(barcodes = "CGACGTGTCCTCTAGC-1", query = data.table()) :
## Both 'barcodes' and 'query' parameters cannot be used. Use method 'grab_bx()' by a character vector of BX barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details.
expect_error(foo$grab_bx(barcodes='CGACGTGTCCTCTAGC-1', query=data.table(), verbose=TRUE))
expect_error(foo$grab_bx(barcodes='CGACGTGTCCTCTAGC-1', query=GRanges("chr5:1053000-1253655", verbose=TRUE)))
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(foo$grab_bx(barcodes='2'), NA)
expect_equal(foo$grab_bx(barcodes='foobar'), NA)
## multiple barcodes
expect_equal(length(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), mc.cores=2, verbose=TRUE)), 8)
expect_equal(length(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), mc.cores=2, verbose=TRUE, data.table=TRUE)), 22)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 8)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[2], 22)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(length(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1', 'foo', 'foobar', '2'), mc.cores=2)), 8)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 8)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 22)
##
## if (!inherits(barcodes, "character"))
## Error in foo$grab_bx(barcodes = 2) :
## Invalid barcodes. Input 'barcodes' must be a character vector. Must provide barcode with input BAM.
expect_error(foo$grab_bx(barcodes=2))
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(foo$grab_bx(query=c('foo')))
##
## if (length(query)==0){
expect_equal(foo$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("chr5:1053000-1253655")), NA)
expect_equal(foo$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("chr5:1053000-1253655"), data.table=TRUE), NA)
##
## else
expect_equal(length(foo$grab_bx(query=GRanges('chr19:27842400-27842700'), verbose=TRUE)), 4)
##
## data.table = TRUE
expect_equal(dim(foo$grab_bx(query=GRanges('chr19:27842400-27842700'), verbose=TRUE, data.table=TRUE))[1], 4)
##
## try data.frame
expect_equal(length(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(length(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
##
## try data.table
expect_equal(length(foo$grab_bx(query=as.data.table(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(length(foo$grab_bx(query=as.data.table(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
##
## check UCSC/Ensembl conversion
expect_equal(foo$grab_bx(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("5:1053000-1253655")), NA)
expect_equal(foo$grab_bx(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("5:1053000-1253655"), data.table=TRUE), NA)
foo_ensembl = bambi$new(bam_file = example_bam_Ensembl)
expect_equal(foo_ensembl$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foo_ensembl$grab_bx(query=GRanges("chr5:1053000-1253655")), NA)
expect_equal(foo_ensembl$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo_ensembl$grab_bx(query=GRanges("chr5:1053000-1253655"), data.table=TRUE), NA)
##
## else
expect_equal(length(foo$grab_bx(query=GRanges('19:27842400-27842700'), verbose=TRUE)), 4)
expect_equal(length(foo$grab_bx(query=GRanges('chr19:27842400-27842700'), verbose=TRUE)), 4)
expect_equal(dim(foo$grab_bx(query=GRanges('19:27842400-27842700'), verbose=TRUE, data.table=TRUE))[1], 4)
})
## CB
## 'GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'
## TCCCGATCACCAGTTA-1
## AGGTCCGAGGTACTCT-1
test_that('bambi test method grab_cb()', {
## check works
foocb = bambi$new(bam_file = example_CB_bam)
## Error in foo$grab_cb() :
## BX is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foocb$grab_bx())
## UB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foocb$grab_ub())
###
## somehow having an issue as it's a vector...
## expect_equal(foocb$grab_cb('GTAGTCATCTGGGCCA-1'))$flag, 16)
## expect_equal(foocb$grab_cb('GTAGTCATCTGGGCCA-1'))$mapq, 255)
## expect_match(foocb$grab_cb('GTAGTCATCTGGGCCA-1'))$cigar, "98M")
expect_equal(length(foocb$grab_cb('GTAGTCATCTGGGCCA-1')), 1)
expect_equal(length(foocb$grab_cb('GTAGTCATCTGGGCCA-1', verbose=TRUE)), 1)
expect_equal(length(foocb$grab_cb('GTAGTCATCTGGGCCA-1', data.table=TRUE)), 1)
##expect_equal(as.numeric(dim(foocb$grab_cb('GTAGTCATCTGGGCCA-1', data.table=TRUE)))[1], 1)
##expect_equal(dim(foocb$grab_cb('GTAGTCATCTGGGCCA-1', data.table=TRUE))[2], 25)
##
## if ((is.null(barcodes)) & (is.null(query))){
expect_equal(foocb$grab_cb(), GRanges())
expect_equal(foocb$grab_cb(data.table=TRUE), data.table())
##
## if ((!is.null(barcodes)) & (!is.null(query))){
## Error in foo$grab_bx(barcodes = "CGACGTGTCCTCTAGC-1", query = data.table()) :
## Both 'barcodes' and 'query' parameters cannot be used. Use method 'grab_bx()' by a character vector of BX barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details.
expect_error(foocb$grab_cb(barcodes='GTAGTCATCTGGGCCA-1', query=data.table(), verbose=TRUE))
expect_error(foocb$grab_cb(barcodes='GTAGTCATCTGGGCCA-1', query=GRanges("chr5:1053000-1253655"), verbose=TRUE))
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(foocb$grab_cb(barcodes='2'), NA)
expect_equal(foocb$grab_cb(barcodes='foobar'), NA)
##
## multiple barcodes
expect_equal(length(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'), mc.cores=2, verbose=TRUE)), 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'), data.table=TRUE, mc.cores=2))[2], 26)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(length(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1', 'foo', 'foobar', '2'), mc.cores=2)), 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 26)
##
## if (!inherits(barcodes, "character"))
## Invalid barcodes. Input 'barcodes' must be a character vector. Must provide barcode with input BAM.
expect_error(foocb$grab_cb(barcodes=2))
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(foocb$grab_cb(query=c('foo')))
##
## if (length(query)==0){
expect_equal(foocb$grab_cb(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
##
## data.table = TRUE
expect_equal(dim(foocb$grab_cb(query=GRanges("19:1440000-1440500"), verbose=TRUE, data.table = TRUE))[1], 33)
## else
expect_equal(length(foocb$grab_cb(query=GRanges("19:1440000-1440500"), verbose=TRUE)), 33)
##
## try data.frame
expect_equal(length(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 33)
expect_equal(length(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
##
## try data.table
expect_equal(length(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 33)
expect_equal(length(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
##
## check UCSC/Ensembl conversion
expect_equal(foocb$grab_cb(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges("chr5:1053000-1253655"), verbose=TRUE), NA)
####expect_equal(foocb$grab_cb(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(foocb$grab_cb(query=GRanges("chr5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
foocb_ucsc = bambi$new(bam_file = example_CB_bam_UCSC)
expect_equal(foocb_ucsc$grab_cb(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foocb_ucsc$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE), NA)
####expect_equal(foocb_ucsc$grab_cb(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(foocb_ucsc$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
##
## else
expect_equal(length(foocb$grab_cb(query=GRanges("chr19:1440000-1440500"), verbose=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=GRanges("chr19:1440000-1440500"), verbose=TRUE, data.table=TRUE))[1], 33)
})
## UB
## ATACAAGCGG
## CGGAGGACGT
## CATAGCGTTT
## 'ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT'
test_that('bambi test method grab_ub()', {
## check works
fooub = bambi$new(bam_file = example_UB_bam)
## Error in foo$grab_cb() :
## BX is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(fooub$grab_bx())
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(fooub$grab_cb())
###
## expect_equal(as.data.frame(fooub$grab_ub('ATACAAGCGG', verbose=TRUE))$flag, 0)
## expect_equal(as.data.frame(fooub$grab_ub('ATACAAGCGG'))$mapq, 255)
## expect_match(as.data.frame(fooub$grab_ub('ATACAAGCGG'))$cigar, "98M")
expect_equal(length(fooub$grab_ub('ATACAAGCGG')), 1)
expect_equal(length(fooub$grab_ub('ATACAAGCGG', verbose=TRUE)), 1)
expect_equal(length(fooub$grab_ub('ATACAAGCGG', verbose=TRUE, data.table=TRUE)), 1)
## expect_equal(as.numeric(dim(fooub$grab_ub('ATACAAGCGG', verbose=TRUE, data.table=TRUE)))[1], 1)
## expect_equal(dim(fooub$grab_ub('ATACAAGCGG', verbose=TRUE, data.table=TRUE))[2], 25)
##
## if ((is.null(barcodes)) & (is.null(query))){
expect_equal(fooub$grab_ub(), GRanges())
expect_equal(fooub$grab_ub(data.table=TRUE), data.table())
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(fooub$grab_ub(barcodes='2'), NA)
expect_equal(fooub$grab_ub(barcodes='foobar'), NA)
##
## if ((!is.null(barcodes)) & (!is.null(query))){
## Error in foo$grab_bx(barcodes = "CGACGTGTCCTCTAGC-1", query = data.table()) :
## Both 'barcodes' and 'query' parameters cannot be used. Use method 'grab_bx()' by a character vector of BX barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details.
expect_error(fooub$grab_ub(barcodes='ATACAAGCGG', query=data.table()))
expect_error(fooub$grab_ub(barcodes='ATACAAGCGG', query=GRanges("chr5:1053000-1253655")))
##
## multiple barcodes
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 0)
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT'), data.table=TRUE, mc.cores=2, verbose=TRUE))[2], 12)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 0)
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 12)
##
## if (!inherits(barcodes, "character"))
## Invalid barcodes. Input 'barcodes' must be a character vector. Must provide barcode with input BAM.
expect_error(fooub$grab_ub(barcodes=2))
## if ((is.null(barcodes)) & (!is.null(query))){
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(fooub$grab_ub(query=c('foo')))
##
## if (length(query)==0){
expect_equal(fooub$grab_ub(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(fooub$grab_ub(query=GRanges("5:1053000-1253655")), NA)
expect_equal(fooub$grab_ub(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(fooub$grab_ub(query=GRanges("5:1053000-1253655"), data.table=TRUE), NA)
##
## else
expect_equal(length(fooub$grab_ub(query=GRanges("19:1440000-1440500"), verbose=TRUE)), 2)
##
## data.table = TRUE
expect_equal(dim(fooub$grab_ub(query=GRanges("19:1440000-1440500"), verbose=TRUE, data.table = TRUE))[1], 2)
##
## try data.frame input
expect_equal(length(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 2)
expect_equal(length(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
##
## try data.table
expect_equal(length(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 2)
expect_equal(length(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
##
## check UCSC/Ensembl conversion
expect_equal(fooub$grab_ub(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(fooub$grab_ub(query=GRanges("chr5:1053000-1253655")), NA)
####expect_equal(fooub$grab_ub(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(fooub$grab_ub(query=GRanges("chr5:1053000-1253655", data.table=TRUE)), NA)
fooub_ucsc = bambi$new(bam_file = example_UB_bam_UCSC)
expect_equal(fooub_ucsc$grab_ub(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(fooub_ucsc$grab_ub(query=GRanges("5:1053000-1253655")), NA)
####expect_equal(fooub_ucsc$grab_ub(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(fooub_ucsc$grab_ub(query=GRanges("5:1053000-1253655", data.table=TRUE)), NA)
##
expect_equal(length(fooub$grab_ub(query=GRanges("chr19:1440000-1440500"), verbose=TRUE)), 2)
####expect_equal(length(fooub$grab_ub(query=GRanges("chr19:1440000-1440500"), verbose=TRUE, data.table=TRUE)), 2)
})
## another tag, e.g. PS from HCC1143
## fetch_by_tag = function(tag, tag_queries=NULL, query=NULL, data.table=FALSE, verbose=FALSE, mc.cores=1)
test_that('bambi test method fetch_by_tag()', {
## check works
foo_fetch_bx = bambi$new(bam_file = example_bam)
## Error in foo$grab_cb() :
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo_fetch_bx$grab_cb())
##
## Error in foo_fetch_bx$fetch_by_tag(tag = c("BX", "CB")) :
## Invalid tag input. Multiple tags at once is not currently supported with 'fetch_by_tag()'. Please see documentation for details.
expect_error(foo_fetch_bx$fetch_by_tag(tag = c('BX', 'CB')))
##
## if (!inherits(tag, "character")){
## stop("Invalid tag. Input 'tag' must be a single character string. Must provide valid BAM field.")
## }
## Invalid tag. Input 'tag' must be a single character string. Must provide valid BAM field.
expect_error(foo_fetch_bx$fetch_by_tag(tag = 42))
##
## foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[1], 97)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[2], 145)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$mapq[1], 60)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$mapq[2], 60)
expect_match(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$cigar[1], "80M47S")
expect_match(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$cigar[2], "37S113M")
expect_equal(length(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')), 2)
expect_equal(length(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', data.table=TRUE)), 23)
##
## if (check_index(self$bamdb_path, tag) != TRUE){
## Error in foo_fetch_bx$fetch_by_tag(tag = c("CB")) :
## The input 'tag' is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo_fetch_bx$fetch_by_tag(tag = c('CB')))
##
## if ((!is.null(tag_queries)) & (!is.null(query))){
## Both 'tag_queries' and 'query' parameters cannot be used. Use method 'fetch_by_tag()' by either a character vector of UB barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details
expect_error(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', query=data.table(), verbose=TRUE))
expect_error(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', query=GRanges("chr5:1053000-1253655"), verbose=TRUE))
##
## if ((is.null(tag_queries)) & (is.null(query))){
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX'), GRanges())
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', data.table=TRUE), data.table())
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='2'), NA)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='foobar'), NA)
##
## multiple barcodes
expect_equal(length(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), mc.cores=2, verbose=TRUE)), 8)
expect_equal(dim(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 8)
expect_equal(dim(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[2], 23)
##
##
foo_fetch_ps = bambi$new(bam_file = example_PS_bam)
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo_fetch_ps$grab_cb())
##
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$flag[1], 147)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$flag[2], 1171)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$mapq[1], 60)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$mapq[2], 60)
expect_match(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$cigar[1], "150M")
expect_match(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$cigar[2], "150M")
##
## multiple barcodes
expect_equal(length(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217'), mc.cores=2)), 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217'), data.table=TRUE, mc.cores=2))[1], 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217'), data.table=TRUE, mc.cores=2))[2], 23)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(length(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217', 'foo', 'foobar', '2'), mc.cores=2)), 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 23)
##
## if ((is.null(barcodes)) & (!is.null(query))){
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=c('foo')))
##
## if (length(query)==0){
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:1053000-1253655'), verbose=TRUE), NA)
## data.table = TRUE
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:1053000-1253655'), verbose=TRUE, data.table=TRUE), NA)
##
## else
## FIX
## expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr19:27842400-37842700')), NA)
})
######## utils.R
test_that('countCigar', {
empty_string = 'foobar'
expect_warning(countCigar(empty_string)) ### should be warning message: 'Warning message: In countCigar(example_bam) : NAs introduced by coercion'
expect_equal(dim(countCigar(empty_string))[1], 1)
expect_equal(dim(countCigar(empty_string))[2], 4)
expect_match(colnames(countCigar(empty_string))[1], "D")
expect_match(colnames(countCigar(empty_string))[2], "I")
expect_match(colnames(countCigar(empty_string))[3], "M")
expect_match(colnames(countCigar(empty_string))[4], "S")
expect_equal(countCigar(empty_string)[1], 0)
expect_equal(countCigar(empty_string)[2], 0)
expect_equal(countCigar(empty_string)[3], 0)
expect_equal(countCigar(empty_string)[4], 0)
})
test_that('bamflag', {
gr_example = read.bam(example_bam, all=TRUE)[[42]] ## random GRanges
exdt = as.data.table(gr2dt(gr_example))
## isPaired 1 1
expect_equal(as.data.frame(bamflag(exdt))$isPaired[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isPaired[2], 1)
## error? 'no method for coercing this S4 class to a vector'
##expect_equal(as.data.frame(bamflag(gr_example))$isPaired[1], 1) ## no method for coercing this S4 class to a vector
##expect_equal(as.data.frame(bamflag(gr_example))$isPaired[2], 1)
## isProperPair 1 1
expect_equal(as.data.frame(bamflag(exdt))$isProperPair[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isProperPair[2], 1)
## isUnmappedQuery 0 0
expect_equal(as.data.frame(bamflag(exdt))$isUnmappedQuery[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isUnmappedQuery[2], 0)
## hasUnmappedMate 0 0
expect_equal(as.data.frame(bamflag(exdt))$hasUnmappedMate[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$hasUnmappedMate[2], 0)
## isMinusStrand 0 1
expect_equal(as.data.frame(bamflag(exdt))$isMinusStrand[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isMinusStrand[2], 1)
## isMateMinusStrand 1 0
expect_equal(as.data.frame(bamflag(exdt))$isMateMinusStrand[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isMateMinusStrand[2], 0)
## isFirstMateRead 1 0
expect_equal(as.data.frame(bamflag(exdt))$isFirstMateRead[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isFirstMateRead[2], 1)
## isSecondMateRead 0 1
expect_equal(as.data.frame(bamflag(exdt))$isSecondMateRead[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isSecondMateRead[2], 0)
## isNotPrimaryRead 0 0
expect_equal(as.data.frame(bamflag(exdt))$isNotPrimaryRead[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isNotPrimaryRead[2], 0)
## isNotPassingQualityControls 0 0
expect_equal(as.data.frame(bamflag(exdt))$isNotPassingQualityControls[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isNotPassingQualityControls[2], 0)
## isDuplicate 0 0
expect_equal(as.data.frame(bamflag(exdt))$isDuplicate[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isDuplicate[2], 0)
## isSupplementary 0 0
expect_equal(as.data.frame(bamflag(exdt))$isSupplementary[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isSupplementary[2], 0)
})
## parse_outputs
test_that('parse_outputs', {
## generate an example output from query_bam_index()
## should output a DataFrame with columns "qname", "flag", "rname", "pos", "mapq", "cigar", "rnext", "pnext", "tlen", "seq", "qual"
foo = read.bam(example_bam, all=TRUE)
gr2 = foo[[2]]
dt2 = gr2dt(gr2)
## correct how scanBam() names BAM fields
dt2$rnext = dt2$mrnm
dt2$pnext = dt2$mpos
dt2$tlen = dt2$isize
dt2$rname = dt2$seqnames
dt2$mrnm = NULL
dt2$mpos = NULL
dt2$isize = NULL
dt2$MD = NULL
dt2$MQ = NULL
dt2$seqnames = NULL
dt2$pos = dt2$start
dt2$start = NULL
dt2$end = NULL
dt2$strand = NULL
dt2$width = NULL
dt2$qwidth = NULL
output_list = as.list(dt2) ## list with 11 mandatory BAM fields
## > names(output_list)
## [1] "qname" "flag" "qwidth" "mapq" "cigar" "seq" "qual" "rnext"
## [9] "pnext" "tlen" "rname" "pos"
expect_equal(width(parse_outputs(output_list))[1], 82)
expect_equal(width(parse_outputs(output_list))[2], 150)
expect_match(as.character(seqnames(parse_outputs(output_list))[1]), "chr19")
expect_match(as.character(seqnames(parse_outputs(output_list))[2]), "chr19")
})
## check_index
test_that('check_index', {
expect_true(check_index(example_lmdb, "BX"))
expect_true(check_index(example_lmdb, "QNAME"))
expect_false(check_index(example_lmdb, "BZ")) ## only BX and QNAME should be indexed
})
mskilab/bambi documentation built on May 14, 2019, 4:04 a.m.
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library(testthat)
library(bambi)
library(bamUtils)
library(gUtils)
example_bam = 'subset_HCC1143_phased_possorted000005.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_bai = 'subset_HCC1143_phased_possorted000005.bam.bai'
example_lmdb = 'subset_HCC1143_phased_possorted000005_lmdb'
## in Ensembl format, e.g. 5
example_bam_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.bam'
example_bai_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.bam.bai'
example_lmdb_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle_lmdb'
example_CB_bam = 'subset_pbmc8k_possorted_genome_bam000025.CB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_CB_bai = 'subset_pbmc8k_possorted_genome_bam000025.CB.bam.bai'
example_CB_lmdb = 'subset_pbmc8k_possorted_genome_bam000025.CB_lmdb'
## in UCSC format, e.g. 5
example_CB_bam_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_CB_bai_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB.bam.bai'
example_CB_lmdb_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB_lmdb'
example_UB_bam = 'subset_pbmc8k_possorted_genome_bam000025.UB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_UB_bai = 'subset_pbmc8k_possorted_genome_bam000025.UB.bam.bai'
example_UB_lmdb = 'subset_pbmc8k_possorted_genome_bam000025.UB_lmdb'
## in UCSC format, e.g. 5
example_UB_bam_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_UB_bai_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB.bam.bai'
example_UB_lmdb_UCSC = 'subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB_lmd'
example_PS_bam = 'subset_HCC1143_phased_possorted000005.PS.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_PS_bai = 'subset_HCC1143_phased_possorted000005.PS.bam.bai'
example_PS_lmdb = 'subset_HCC1143_phased_possorted000005.PS_lmdb'
## in Ensembl format, e.g. chr5
example_PS_bam_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.PS.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_PS_bai_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.PS.bam.bai'
example_PS_lmdb_Ensembl = 'subset_HCC1143_phased_possorted000005.EnsemblStyle.PS_lmdb'
bam_no_lmdb = 'bam_with_no_lmdb.bam'
######## R6_class.R
test_that('bambi class constructor', {
## Error in .subset2(public_bind_env, "initialize")(...) :
## BAM file not found. A valid BAM for 'bam_file' must be provided.
expect_error(bambi$new(bam_file = 'foobar'))
## Error in .subset2(public_bind_env, "initialize")(...) :
## Cannot open BAM. A valid BAM for 'bam_file' must be provided.
expect_error(bambi$new(bam_file = 'fake_bam.txt'))
## if (is.null(bamdb_path))
## Error in .subset2(public_bind_env, "initialize")(...) :
## Error: Pathname to bamdb LMDB subdirectory must be provided
expect_error(bambi$new(bam_file ='bam_with_no_lmdb.bam'))
## valid
foo = bambi$new(bam_file = example_bam)
expect_match(foo$bam_file, 'subset_HCC1143_phased_possorted000005.bam')
expect_match(foo$bamdb_path, 'subset_HCC1143_phased_possorted000005_lmdb')
})
test_that('bambi test method grab_bx()', {
## check works
foo = bambi$new(bam_file = example_bam)
## Error in foo$grab_cb() :
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo$grab_cb())
## UB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo$grab_ub())
###
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[1], 97)
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[2], 145)
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$mapq[1], 60)
expect_equal(foo$grab_bx('CGGCTAGGTAGAATAC-1', verbose=TRUE)$mapq[2], 60)
expect_match(foo$grab_bx('CGGCTAGGTAGAATAC-1')$cigar[1], "80M47S")
expect_match(foo$grab_bx('CGGCTAGGTAGAATAC-1')$cigar[2], "37S113M")
expect_equal(length(foo$grab_bx('CGGCTAGGTAGAATAC-1')), 2)
expect_equal(length(foo$grab_bx('CGGCTAGGTAGAATAC-1', data.table=TRUE)), 22)
##
## if ((is.null(barcodes)) & (is.null(query))){
expect_equal(foo$grab_bx(), GRanges())
expect_equal(foo$grab_bx(data.table=TRUE), data.table())
##
## if ((!is.null(barcodes)) & (!is.null(query))){
## Error in foo$grab_bx(barcodes = "CGACGTGTCCTCTAGC-1", query = data.table()) :
## Both 'barcodes' and 'query' parameters cannot be used. Use method 'grab_bx()' by a character vector of BX barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details.
expect_error(foo$grab_bx(barcodes='CGACGTGTCCTCTAGC-1', query=data.table(), verbose=TRUE))
expect_error(foo$grab_bx(barcodes='CGACGTGTCCTCTAGC-1', query=GRanges("chr5:1053000-1253655", verbose=TRUE)))
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(foo$grab_bx(barcodes='2'), NA)
expect_equal(foo$grab_bx(barcodes='foobar'), NA)
## multiple barcodes
expect_equal(length(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), mc.cores=2, verbose=TRUE)), 8)
expect_equal(length(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), mc.cores=2, verbose=TRUE, data.table=TRUE)), 22)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 8)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[2], 22)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(length(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1', 'foo', 'foobar', '2'), mc.cores=2)), 8)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 8)
expect_equal(dim(foo$grab_bx(barcodes=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 22)
##
## if (!inherits(barcodes, "character"))
## Error in foo$grab_bx(barcodes = 2) :
## Invalid barcodes. Input 'barcodes' must be a character vector. Must provide barcode with input BAM.
expect_error(foo$grab_bx(barcodes=2))
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(foo$grab_bx(query=c('foo')))
##
## if (length(query)==0){
expect_equal(foo$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("chr5:1053000-1253655")), NA)
expect_equal(foo$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("chr5:1053000-1253655"), data.table=TRUE), NA)
##
## else
expect_equal(length(foo$grab_bx(query=GRanges('chr19:27842400-27842700'), verbose=TRUE)), 4)
##
## data.table = TRUE
expect_equal(dim(foo$grab_bx(query=GRanges('chr19:27842400-27842700'), verbose=TRUE, data.table=TRUE))[1], 4)
##
## try data.frame
expect_equal(length(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(length(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
##
## try data.table
expect_equal(length(foo$grab_bx(query=as.data.table(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(length(foo$grab_bx(query=as.data.table(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE)), 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('chr19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
expect_equal(dim(foo$grab_bx(query=as.data.frame(gr2dt(GRanges('19:27842400-27842700'))), verbose=TRUE, data.table=TRUE))[1], 4)
##
## check UCSC/Ensembl conversion
expect_equal(foo$grab_bx(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("5:1053000-1253655")), NA)
expect_equal(foo$grab_bx(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo$grab_bx(query=GRanges("5:1053000-1253655"), data.table=TRUE), NA)
foo_ensembl = bambi$new(bam_file = example_bam_Ensembl)
expect_equal(foo_ensembl$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foo_ensembl$grab_bx(query=GRanges("chr5:1053000-1253655")), NA)
expect_equal(foo_ensembl$grab_bx(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo_ensembl$grab_bx(query=GRanges("chr5:1053000-1253655"), data.table=TRUE), NA)
##
## else
expect_equal(length(foo$grab_bx(query=GRanges('19:27842400-27842700'), verbose=TRUE)), 4)
expect_equal(length(foo$grab_bx(query=GRanges('chr19:27842400-27842700'), verbose=TRUE)), 4)
expect_equal(dim(foo$grab_bx(query=GRanges('19:27842400-27842700'), verbose=TRUE, data.table=TRUE))[1], 4)
})
## CB
## 'GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'
## TCCCGATCACCAGTTA-1
## AGGTCCGAGGTACTCT-1
test_that('bambi test method grab_cb()', {
## check works
foocb = bambi$new(bam_file = example_CB_bam)
## Error in foo$grab_cb() :
## BX is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foocb$grab_bx())
## UB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foocb$grab_ub())
###
## somehow having an issue as it's a vector...
## expect_equal(foocb$grab_cb('GTAGTCATCTGGGCCA-1'))$flag, 16)
## expect_equal(foocb$grab_cb('GTAGTCATCTGGGCCA-1'))$mapq, 255)
## expect_match(foocb$grab_cb('GTAGTCATCTGGGCCA-1'))$cigar, "98M")
expect_equal(length(foocb$grab_cb('GTAGTCATCTGGGCCA-1')), 1)
expect_equal(length(foocb$grab_cb('GTAGTCATCTGGGCCA-1', verbose=TRUE)), 1)
expect_equal(length(foocb$grab_cb('GTAGTCATCTGGGCCA-1', data.table=TRUE)), 1)
##expect_equal(as.numeric(dim(foocb$grab_cb('GTAGTCATCTGGGCCA-1', data.table=TRUE)))[1], 1)
##expect_equal(dim(foocb$grab_cb('GTAGTCATCTGGGCCA-1', data.table=TRUE))[2], 25)
##
## if ((is.null(barcodes)) & (is.null(query))){
expect_equal(foocb$grab_cb(), GRanges())
expect_equal(foocb$grab_cb(data.table=TRUE), data.table())
##
## if ((!is.null(barcodes)) & (!is.null(query))){
## Error in foo$grab_bx(barcodes = "CGACGTGTCCTCTAGC-1", query = data.table()) :
## Both 'barcodes' and 'query' parameters cannot be used. Use method 'grab_bx()' by a character vector of BX barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details.
expect_error(foocb$grab_cb(barcodes='GTAGTCATCTGGGCCA-1', query=data.table(), verbose=TRUE))
expect_error(foocb$grab_cb(barcodes='GTAGTCATCTGGGCCA-1', query=GRanges("chr5:1053000-1253655"), verbose=TRUE))
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(foocb$grab_cb(barcodes='2'), NA)
expect_equal(foocb$grab_cb(barcodes='foobar'), NA)
##
## multiple barcodes
expect_equal(length(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'), mc.cores=2, verbose=TRUE)), 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1'), data.table=TRUE, mc.cores=2))[2], 26)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(length(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1', 'foo', 'foobar', '2'), mc.cores=2)), 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 10)
expect_equal(dim(foocb$grab_cb(barcodes=c('GTAGTCATCTGGGCCA-1', 'TCCCGATCACCAGTTA-1', 'AGGTCCGAGGTACTCT-1', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 26)
##
## if (!inherits(barcodes, "character"))
## Invalid barcodes. Input 'barcodes' must be a character vector. Must provide barcode with input BAM.
expect_error(foocb$grab_cb(barcodes=2))
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(foocb$grab_cb(query=c('foo')))
##
## if (length(query)==0){
expect_equal(foocb$grab_cb(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
##
## data.table = TRUE
expect_equal(dim(foocb$grab_cb(query=GRanges("19:1440000-1440500"), verbose=TRUE, data.table = TRUE))[1], 33)
## else
expect_equal(length(foocb$grab_cb(query=GRanges("19:1440000-1440500"), verbose=TRUE)), 33)
##
## try data.frame
expect_equal(length(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 33)
expect_equal(length(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
##
## try data.table
expect_equal(length(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 33)
expect_equal(length(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 33)
##
## check UCSC/Ensembl conversion
expect_equal(foocb$grab_cb(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foocb$grab_cb(query=GRanges("chr5:1053000-1253655"), verbose=TRUE), NA)
####expect_equal(foocb$grab_cb(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(foocb$grab_cb(query=GRanges("chr5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
foocb_ucsc = bambi$new(bam_file = example_CB_bam_UCSC)
expect_equal(foocb_ucsc$grab_cb(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(foocb_ucsc$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE), NA)
####expect_equal(foocb_ucsc$grab_cb(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(foocb_ucsc$grab_cb(query=GRanges("5:1053000-1253655"), verbose=TRUE, data.table=TRUE), NA)
##
## else
expect_equal(length(foocb$grab_cb(query=GRanges("chr19:1440000-1440500"), verbose=TRUE)), 33)
####expect_equal(dim(foocb$grab_cb(query=GRanges("chr19:1440000-1440500"), verbose=TRUE, data.table=TRUE))[1], 33)
})
## UB
## ATACAAGCGG
## CGGAGGACGT
## CATAGCGTTT
## 'ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT'
test_that('bambi test method grab_ub()', {
## check works
fooub = bambi$new(bam_file = example_UB_bam)
## Error in foo$grab_cb() :
## BX is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(fooub$grab_bx())
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(fooub$grab_cb())
###
## expect_equal(as.data.frame(fooub$grab_ub('ATACAAGCGG', verbose=TRUE))$flag, 0)
## expect_equal(as.data.frame(fooub$grab_ub('ATACAAGCGG'))$mapq, 255)
## expect_match(as.data.frame(fooub$grab_ub('ATACAAGCGG'))$cigar, "98M")
expect_equal(length(fooub$grab_ub('ATACAAGCGG')), 1)
expect_equal(length(fooub$grab_ub('ATACAAGCGG', verbose=TRUE)), 1)
expect_equal(length(fooub$grab_ub('ATACAAGCGG', verbose=TRUE, data.table=TRUE)), 1)
## expect_equal(as.numeric(dim(fooub$grab_ub('ATACAAGCGG', verbose=TRUE, data.table=TRUE)))[1], 1)
## expect_equal(dim(fooub$grab_ub('ATACAAGCGG', verbose=TRUE, data.table=TRUE))[2], 25)
##
## if ((is.null(barcodes)) & (is.null(query))){
expect_equal(fooub$grab_ub(), GRanges())
expect_equal(fooub$grab_ub(data.table=TRUE), data.table())
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(fooub$grab_ub(barcodes='2'), NA)
expect_equal(fooub$grab_ub(barcodes='foobar'), NA)
##
## if ((!is.null(barcodes)) & (!is.null(query))){
## Error in foo$grab_bx(barcodes = "CGACGTGTCCTCTAGC-1", query = data.table()) :
## Both 'barcodes' and 'query' parameters cannot be used. Use method 'grab_bx()' by a character vector of BX barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details.
expect_error(fooub$grab_ub(barcodes='ATACAAGCGG', query=data.table()))
expect_error(fooub$grab_ub(barcodes='ATACAAGCGG', query=GRanges("chr5:1053000-1253655")))
##
## multiple barcodes
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 0)
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT'), data.table=TRUE, mc.cores=2, verbose=TRUE))[2], 12)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 0)
expect_equal(dim(fooub$grab_ub(barcodes=c('ATACAAGCGG', 'CGGAGGACGT', 'CATAGCGTTT', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 12)
##
## if (!inherits(barcodes, "character"))
## Invalid barcodes. Input 'barcodes' must be a character vector. Must provide barcode with input BAM.
expect_error(fooub$grab_ub(barcodes=2))
## if ((is.null(barcodes)) & (!is.null(query))){
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(fooub$grab_ub(query=c('foo')))
##
## if (length(query)==0){
expect_equal(fooub$grab_ub(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(fooub$grab_ub(query=GRanges("5:1053000-1253655")), NA)
expect_equal(fooub$grab_ub(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(fooub$grab_ub(query=GRanges("5:1053000-1253655"), data.table=TRUE), NA)
##
## else
expect_equal(length(fooub$grab_ub(query=GRanges("19:1440000-1440500"), verbose=TRUE)), 2)
##
## data.table = TRUE
expect_equal(dim(fooub$grab_ub(query=GRanges("19:1440000-1440500"), verbose=TRUE, data.table = TRUE))[1], 2)
##
## try data.frame input
expect_equal(length(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 2)
expect_equal(length(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.frame(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
##
## try data.table
expect_equal(length(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("19:1440000-1440500"))), verbose=TRUE)), 2)
expect_equal(length(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500"))), verbose=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
####expect_equal(dim(fooub$grab_ub(query=as.data.table(gr2dt(GRanges("chr19:1440000-1440500")))[1], verbose=TRUE, data.table=TRUE)), 2)
##
## check UCSC/Ensembl conversion
expect_equal(fooub$grab_ub(query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(fooub$grab_ub(query=GRanges("chr5:1053000-1253655")), NA)
####expect_equal(fooub$grab_ub(query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(fooub$grab_ub(query=GRanges("chr5:1053000-1253655", data.table=TRUE)), NA)
fooub_ucsc = bambi$new(bam_file = example_UB_bam_UCSC)
expect_equal(fooub_ucsc$grab_ub(query=GRanges('5:10-15'), verbose=TRUE), NA)
expect_equal(fooub_ucsc$grab_ub(query=GRanges("5:1053000-1253655")), NA)
####expect_equal(fooub_ucsc$grab_ub(query=GRanges('5:10-15'), verbose=TRUE, data.table=TRUE), NA)
####expect_equal(fooub_ucsc$grab_ub(query=GRanges("5:1053000-1253655", data.table=TRUE)), NA)
##
expect_equal(length(fooub$grab_ub(query=GRanges("chr19:1440000-1440500"), verbose=TRUE)), 2)
####expect_equal(length(fooub$grab_ub(query=GRanges("chr19:1440000-1440500"), verbose=TRUE, data.table=TRUE)), 2)
})
## another tag, e.g. PS from HCC1143
## fetch_by_tag = function(tag, tag_queries=NULL, query=NULL, data.table=FALSE, verbose=FALSE, mc.cores=1)
test_that('bambi test method fetch_by_tag()', {
## check works
foo_fetch_bx = bambi$new(bam_file = example_bam)
## Error in foo$grab_cb() :
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo_fetch_bx$grab_cb())
##
## Error in foo_fetch_bx$fetch_by_tag(tag = c("BX", "CB")) :
## Invalid tag input. Multiple tags at once is not currently supported with 'fetch_by_tag()'. Please see documentation for details.
expect_error(foo_fetch_bx$fetch_by_tag(tag = c('BX', 'CB')))
##
## if (!inherits(tag, "character")){
## stop("Invalid tag. Input 'tag' must be a single character string. Must provide valid BAM field.")
## }
## Invalid tag. Input 'tag' must be a single character string. Must provide valid BAM field.
expect_error(foo_fetch_bx$fetch_by_tag(tag = 42))
##
## foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[1], 97)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', verbose=TRUE)$flag[2], 145)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$mapq[1], 60)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$mapq[2], 60)
expect_match(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$cigar[1], "80M47S")
expect_match(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')$cigar[2], "37S113M")
expect_equal(length(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1')), 2)
expect_equal(length(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', data.table=TRUE)), 23)
##
## if (check_index(self$bamdb_path, tag) != TRUE){
## Error in foo_fetch_bx$fetch_by_tag(tag = c("CB")) :
## The input 'tag' is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo_fetch_bx$fetch_by_tag(tag = c('CB')))
##
## if ((!is.null(tag_queries)) & (!is.null(query))){
## Both 'tag_queries' and 'query' parameters cannot be used. Use method 'fetch_by_tag()' by either a character vector of UB barcodes, or a GRanges/data.table of a genomic region. Please see documentation for details
expect_error(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', query=data.table(), verbose=TRUE))
expect_error(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='CGGCTAGGTAGAATAC-1', query=GRanges("chr5:1053000-1253655"), verbose=TRUE))
##
## if ((is.null(tag_queries)) & (is.null(query))){
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX'), GRanges())
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', data.table=TRUE), data.table())
##
## empty query: R standard is NULL for error, NA for no rows returned
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='2'), NA)
expect_equal(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries='foobar'), NA)
##
## multiple barcodes
expect_equal(length(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), mc.cores=2, verbose=TRUE)), 8)
expect_equal(dim(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[1], 8)
expect_equal(dim(foo_fetch_bx$fetch_by_tag(tag = 'BX', tag_queries=c('CGGCTAGGTAGAATAC-1', 'AGCTTCCCACTTCACC-1', 'GGCGTTGAGAGCTGGT-1'), data.table=TRUE, mc.cores=2, verbose=TRUE))[2], 23)
##
##
foo_fetch_ps = bambi$new(bam_file = example_PS_bam)
## CB is not contained as an LMDB key in 'bamdb_path'. Please see documentation for details.
expect_error(foo_fetch_ps$grab_cb())
##
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$flag[1], 147)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$flag[2], 1171)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$mapq[1], 60)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$mapq[2], 60)
expect_match(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$cigar[1], "150M")
expect_match(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries='1013620572')$cigar[2], "150M")
##
## multiple barcodes
expect_equal(length(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217'), mc.cores=2)), 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217'), data.table=TRUE, mc.cores=2))[1], 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217'), data.table=TRUE, mc.cores=2))[2], 23)
##
## If there are "empty row" queries, I currently return nothing
expect_equal(length(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217', 'foo', 'foobar', '2'), mc.cores=2)), 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[1], 47)
expect_equal(dim(foo_fetch_ps$fetch_by_tag(tag = 'PS', tag_queries=c('10522462', '1013620572', '870145439217', 'foo', 'foobar', '2'), data.table=TRUE, mc.cores=2))[2], 23)
##
## if ((is.null(barcodes)) & (!is.null(query))){
##
## incorrect query
## stop("Invalid query. Input 'query' must be a data.table, data.frame or GRanges.")
expect_error(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=c('foo')))
##
## if (length(query)==0){
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:10-15'), verbose=TRUE), NA)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:1053000-1253655'), verbose=TRUE), NA)
## data.table = TRUE
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:10-15'), verbose=TRUE, data.table=TRUE), NA)
expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr5:1053000-1253655'), verbose=TRUE, data.table=TRUE), NA)
##
## else
## FIX
## expect_equal(foo_fetch_ps$fetch_by_tag(tag = 'PS', query=GRanges('chr19:27842400-37842700')), NA)
})
######## utils.R
test_that('countCigar', {
empty_string = 'foobar'
expect_warning(countCigar(empty_string)) ### should be warning message: 'Warning message: In countCigar(example_bam) : NAs introduced by coercion'
expect_equal(dim(countCigar(empty_string))[1], 1)
expect_equal(dim(countCigar(empty_string))[2], 4)
expect_match(colnames(countCigar(empty_string))[1], "D")
expect_match(colnames(countCigar(empty_string))[2], "I")
expect_match(colnames(countCigar(empty_string))[3], "M")
expect_match(colnames(countCigar(empty_string))[4], "S")
expect_equal(countCigar(empty_string)[1], 0)
expect_equal(countCigar(empty_string)[2], 0)
expect_equal(countCigar(empty_string)[3], 0)
expect_equal(countCigar(empty_string)[4], 0)
})
test_that('bamflag', {
gr_example = read.bam(example_bam, all=TRUE)[[42]] ## random GRanges
exdt = as.data.table(gr2dt(gr_example))
## isPaired 1 1
expect_equal(as.data.frame(bamflag(exdt))$isPaired[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isPaired[2], 1)
## error? 'no method for coercing this S4 class to a vector'
##expect_equal(as.data.frame(bamflag(gr_example))$isPaired[1], 1) ## no method for coercing this S4 class to a vector
##expect_equal(as.data.frame(bamflag(gr_example))$isPaired[2], 1)
## isProperPair 1 1
expect_equal(as.data.frame(bamflag(exdt))$isProperPair[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isProperPair[2], 1)
## isUnmappedQuery 0 0
expect_equal(as.data.frame(bamflag(exdt))$isUnmappedQuery[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isUnmappedQuery[2], 0)
## hasUnmappedMate 0 0
expect_equal(as.data.frame(bamflag(exdt))$hasUnmappedMate[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$hasUnmappedMate[2], 0)
## isMinusStrand 0 1
expect_equal(as.data.frame(bamflag(exdt))$isMinusStrand[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isMinusStrand[2], 1)
## isMateMinusStrand 1 0
expect_equal(as.data.frame(bamflag(exdt))$isMateMinusStrand[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isMateMinusStrand[2], 0)
## isFirstMateRead 1 0
expect_equal(as.data.frame(bamflag(exdt))$isFirstMateRead[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isFirstMateRead[2], 1)
## isSecondMateRead 0 1
expect_equal(as.data.frame(bamflag(exdt))$isSecondMateRead[1], 1)
expect_equal(as.data.frame(bamflag(exdt))$isSecondMateRead[2], 0)
## isNotPrimaryRead 0 0
expect_equal(as.data.frame(bamflag(exdt))$isNotPrimaryRead[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isNotPrimaryRead[2], 0)
## isNotPassingQualityControls 0 0
expect_equal(as.data.frame(bamflag(exdt))$isNotPassingQualityControls[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isNotPassingQualityControls[2], 0)
## isDuplicate 0 0
expect_equal(as.data.frame(bamflag(exdt))$isDuplicate[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isDuplicate[2], 0)
## isSupplementary 0 0
expect_equal(as.data.frame(bamflag(exdt))$isSupplementary[1], 0)
expect_equal(as.data.frame(bamflag(exdt))$isSupplementary[2], 0)
})
## parse_outputs
test_that('parse_outputs', {
## generate an example output from query_bam_index()
## should output a DataFrame with columns "qname", "flag", "rname", "pos", "mapq", "cigar", "rnext", "pnext", "tlen", "seq", "qual"
foo = read.bam(example_bam, all=TRUE)
gr2 = foo[[2]]
dt2 = gr2dt(gr2)
## correct how scanBam() names BAM fields
dt2$rnext = dt2$mrnm
dt2$pnext = dt2$mpos
dt2$tlen = dt2$isize
dt2$rname = dt2$seqnames
dt2$mrnm = NULL
dt2$mpos = NULL
dt2$isize = NULL
dt2$MD = NULL
dt2$MQ = NULL
dt2$seqnames = NULL
dt2$pos = dt2$start
dt2$start = NULL
dt2$end = NULL
dt2$strand = NULL
dt2$width = NULL
dt2$qwidth = NULL
output_list = as.list(dt2) ## list with 11 mandatory BAM fields
## > names(output_list)
## [1] "qname" "flag" "qwidth" "mapq" "cigar" "seq" "qual" "rnext"
## [9] "pnext" "tlen" "rname" "pos"
expect_equal(width(parse_outputs(output_list))[1], 82)
expect_equal(width(parse_outputs(output_list))[2], 150)
expect_match(as.character(seqnames(parse_outputs(output_list))[1]), "chr19")
expect_match(as.character(seqnames(parse_outputs(output_list))[2]), "chr19")
})
## check_index
test_that('check_index', {
expect_true(check_index(example_lmdb, "BX"))
expect_true(check_index(example_lmdb, "QNAME"))
expect_false(check_index(example_lmdb, "BZ")) ## only BX and QNAME should be indexed
})
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