tests/testthat/test-contigsupport.R

In mskilab/loosends: Classifying loose ends in gGraphs

## library(testthat)
## library(loosends)
## library(gUtils)

## ## reference directory
## ref.dir = "~/git/loosends/inst/extdata/hg19_loosends"
## ref.fasta = "~/git/loosends/inst/extdata/hg19_loosends/human_g1k_v37_decoy.fasta"
## reads.dt.fn = system.file("extdata", "tests", "loosereads_1", "reads.dt.rds", package = "loosends")
## le.dt.fn = system.file("extdata", "tests", "loosereads_1", "le.dt.rds", package = "loosends")
## contig.dt.fn = system.file("extdata", "tests", "loosereads_1", "single.contig.rds", package = "loosends")
## multiple.dt.fn = system.file("extdata", "tests", "loosereads_1", "multiple.contig.rds", package = "loosends")

## ## params
## this.pair = "G32831.HCC1954"
## this.le = parse.gr("20:60158837-")

## ## load saved data
## le.dt = readRDS(le.dt.fn)
## reads.dt = readRDS(reads.dt.fn)
## single.dt = readRDS(contig.dt.fn)
## multiple.dt = readRDS(multiple.dt.fn)

## ## load ref bwa
## ref.obj = grab_ref_obj(ref.dir = ref.dir)

## test_that(desc = "test contig support for single contig", code = {
##     suppressWarnings(
##         expr = {
##             rc = read_support(le.dt = le.dt,
##                               reads.dt = reads.dt,
##                               contigs.dt = single.dt,
##                               ref.bwa = ref.obj$human,
##                               verbose = FALSE)
##                               ## verbose = FALSE)
##             ## expect non-zero unmber of supporting reads
##             expect_true(rc[, .N] > 0)
##             ## expect all reads returned to be supporting reads
##             expect_true(all(rc[, supporting]))
##             expect_true(all(rc[, sample == this.pair]))
##         }
##     )
## })

## ## test_that(desc = "test contig support for single contig with bowtie", code = {
## ##     suppressWarnings(
## ##         expr = {
## ##             rc = read_support(le.dt = le.dt,
## ##                               reads.dt = reads.dt,
## ##                               contigs.dt = single.dt,
## ##                               fasta = ref.fasta, ##pastref.bwa = NULL,ref.obj$human,
## ##                               outdir = "~/testing_tmp/bowtie2_read_support",
## ##                               bowtie = TRUE,
## ##                               verbose = FALSE)
## ##             ## expect non-zero unmber of supporting reads
## ##             expect_true(rc[, .N] > 0)
## ##             ## expect all reads returned to be supporting reads
## ##             expect_true(all(rc[, supporting]))
## ##             expect_true(all(rc[, sample == this.pair]))
## ##         }
## ##     )
## ## })

## test_that(desc = "test contig support wrapper for multiple contigs", code = {
##     suppressWarnings(
##         expr = {
##             rc = read_support_wrapper(le.dt = le.dt,
##                                       reads.dt = reads.dt,
##                                       contigs.dt = multiple.dt,
##                                       id = this.pair,
##                                       ref.bwa = ref.obj$human,
##                                       verbose = FALSE)
##             ## expect number of rows to be equal to number of unique contigs
##             expect_true(rc[, .N] == length(unique(multiple.dt[, qname])))
##             ## expect all leix's to be represented
##             expect_true(all(multiple.dt[, leix] %in% rc[, leix]))
##         }
##     )
## })

## ## test_that(desc = "test contig support wrapper with bowtie", code = {
## ##     suppressWarnings(
## ##         expr = {
## ##             rc = read_support_wrapper(le.dt = le.dt,
## ##                                       reads.dt = reads.dt,
## ##                                       contigs.dt = multiple.dt,
## ##                                       id = this.pair,
## ##                                       ref.bwa = NULL,##ref.obj$human,
## ##                                       ref.fasta = ref.fasta,
## ##                                       bowtie = TRUE,
## ##                                       outdir = "~/testing_tmp/contigsupport/wrapper_bowtie2",
## ##                                       verbose = FALSE)
## ##             ## expect number of rows to be equal to number of unique contigs
## ##             expect_true(rc[, .N] == length(unique(multiple.dt[, qname])))
## ##             ## expect all leix's to be represented
## ##             expect_true(all(multiple.dt[, leix] %in% rc[, leix]))
## ##         }
## ##     )
## ## })