tests/testthat/test-unplaced.R

In arendsee/fagin: Annotate Orphan Genes

context("derive.R")

# fna <- c(
#   #           start         intron   exon   stop
#   paste0("A", "ATG", "CCC", "GATA", "GGG", "TAA", "T", collapse=""),
#   #            stop         intron   exon   start
#   paste0("A", "TTA", "GGG", "CACA", "CCC", "CAT", "T", collapse="")
# ) %>%
#   Biostrings::DNAStringSet() %>%
#   magrittr::set_names(c("foo", "bar"))
#
# gff <- GenomicRanges::GRanges(
#     c("foo", "foo", "bar", "bar"),
#     ranges=IRanges::IRanges(start=c(2,12,2,12), width=c(6,6,6,6)),
#     strand=c('+','+','-','-')
#   )
# GenomicRanges::mcols(gff)$type = "CDS"
# GenomicRanges::mcols(gff)$Parent = c("pan", "pan", "bob", "bob")
#
# cds <- c("ATGGGGCCCTAA", "ATGCCCGGGTAA") %>%
#   Biostrings::DNAStringSet() %>%
#   magrittr::set_names(c("bob", "pan"))
#
# faa <- c("MGP*", "MPG*") %>%
#   Biostrings::AAStringSet() %>%
#   magrittr::set_names(c("bob", "pan"))
#
# test_that("mergeSeqs correctly merges", {
#   expect_true(all( (mergeSeqs(fna, gff, "CDS") %>% esc) == cds))
# })
#
# test_that("dnaregex gracefully handles no matches", {
#   expect_silent(dnaregex(fna, "GANDALF"))
#   expect_true( length(fna[dnaregex(fna, "GANDALF")]) == 0 )
# })
#
# test_that("dnaregex works on all strand variants", {
#   expect_equal(
#     fna[dnaregex(fna, "ATG", strand='b')] %>% as.character %>% as.vector,
#     c("ATG", "CAT")
#   )
#   expect_equal(
#     fna[dnaregex(fna, "ATG", strand='p')] %>% as.character %>% as.vector,
#     "ATG"
#   )
#   expect_equal(
#     fna[dnaregex(fna, "ATG", strand='m')] %>% as.character %>% as.vector,
#     "CAT"
#   )
# })