tests/testthat/test-partis.R

In matsengrp/sumrep: Summary statistics for B cell receptor (BCR) repertoires

library(sumrep)
context("Partis annotations and partitions")

test_data_path <- system.file("extdata", "test_data.fa", package="sumrep")

test_that("sumrep correctly calls partis annotate", {
    dat_a <- getPartisAnnotations(test_data_path, 
                                  do_full_annotation=FALSE,
                                  locus="igh"
                                 )
    "_output" %>% unlink(recursive=TRUE)

    dat_b <- getPartisAnnotations(test_data_path, 
                                  output_filename="blah.csv",
                                  output_path="_output_arbitrary", 
                                  num_procs=8,
                                  locus="igh"
                                 )
    "_output_arbitrary" %>% unlink(recursive=TRUE)

    expect_equal(dat_a %>% names, c("annotations", "mutation_rates"))
    expect_equal(dat_a$mutation_rates[[1]] %>% names, 
                 c("overall_mut_rate", "mut_rate_by_position"))

    expect_equal(ncol(dat_a$annotations), 48)
    expect_equal(nrow(dat_a$annotations), 17)
    expect_equal(ncol(dat_b$annotations), 48)
    expect_equal(nrow(dat_b$annotations), 17)

    dir.create("_output")
    file.create("_output/blah.txt")
    expect_error(getPartisAnnotations(test_data_path))
    "_output" %>% unlink(recursive=TRUE)
})

test_that("sumrep correctly calls partis partition", {
    dat_c <- getPartisPartitions(test_data_path, 
                                 output_filename="blah2.csv",
                                 output_path="_output_arbitrary_again", 
                                 num_procs=8,
                                 locus="igh"
                                )
    "_output_arbitrary_again" %>% unlink(recursive=TRUE)

    expect_equal(nrow(dat_c), 17)
    expect_equal(ncol(dat_c), 38)

    dir.create("_output")
    file.create("_output/blah2.txt")
    expect_error(getPartisPartitions(test_data_path))
    "_output" %>% unlink(recursive=TRUE)
})