Do not test with MHCnuggets locally, due to unsuppressable output, un…

…til fix of richelbilderbeek/mhcnuggetsr#9

R/predict_counts.R

@@ -38,7 +38,7 @@ predict_counts <- function(
   peptide_length,
   percentile,
   verbose = FALSE,
-  ic50_prediction_tool = "mhcnuggetsr"
+  ic50_prediction_tool
 ) {
   testthat::expect_equal(length(protein_sequence), 1)
   empty_tibble <- tibble::tibble(

R/predict_counts_per_proteome.R

@@ -44,7 +44,7 @@ predict_counts_per_proteome <- function(
   peptide_length,
   percentile,
   verbose = FALSE,
-  ic50_prediction_tool = "mhcnuggetsr"
+  ic50_prediction_tool
 ) {
   tibbles <- list()
   for (i in seq_along(protein_sequences)) {

R/predict_n_coincidence_tmh_peptide.R

@@ -30,7 +30,7 @@ predict_n_coincidence_tmh_peptide <- function(# nolint indeed a long function na
   protein_sequence,
   peptide_length,
   verbose = FALSE,
-  ic50_prediction_tool = "mhcnuggetsr"
+  ic50_prediction_tool
 ) {
   bbbq::predict_counts(
     protein_sequence = protein_sequence,

tests/testthat/test-get_ic50_threshold.R

@@ -1,5 +1,5 @@
 test_that("mhcnuggets", {
-
+  if (!pureseqtmr::is_on_travis()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
   expect_silent(

tests/testthat/test-predict_counts.R

@@ -1,4 +1,5 @@
 test_that("MHCNuggets, MHC-I, peptide length 9", {
+  if (!pureseqtmr::is_on_travis()) return()
   if (!pureseqtmr::is_pureseqtm_installed()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
@@ -9,7 +10,8 @@ test_that("MHCNuggets, MHC-I, peptide length 9", {
     protein_sequence = protein_sequence,
     haplotype = get_mhc1_haplotypes()[1],
     peptide_length = 9,
-    percentile = 0.05
+    percentile = 0.05,
+    ic50_prediction_tool = "mhcnuggetsr"
   )
   # Results from verbose output:
   # Table: peptide length: 75, epitope length: 9, n fragments: 67,
@@ -29,6 +31,7 @@ test_that("MHCNuggets, MHC-I, peptide length 9", {
 })
 
 test_that("MHCNuggets, MHC-I, peptide length 10", {
+  if (!pureseqtmr::is_on_travis()) return()
   if (!pureseqtmr::is_pureseqtm_installed()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
@@ -39,7 +42,8 @@ test_that("MHCNuggets, MHC-I, peptide length 10", {
     protein_sequence = protein_sequence,
     haplotype = get_mhc1_haplotypes()[1],
     peptide_length = 10,
-    percentile = 0.05
+    percentile = 0.05,
+    ic50_prediction_tool = "mhcnuggetsr"
   )
   # Results from verbose output:
   # Table: peptide length: 75, epitope length: 9, n fragments: 67,
@@ -59,6 +63,7 @@ test_that("MHCNuggets, MHC-I, peptide length 10", {
 })
 
 test_that("MHCNuggets, MHC-II, peptide length 13", {
+  if (!pureseqtmr::is_on_travis()) return()
   if (!pureseqtmr::is_pureseqtm_installed()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
@@ -69,7 +74,8 @@ test_that("MHCNuggets, MHC-II, peptide length 13", {
     protein_sequence = protein_sequence,
     haplotype = get_mhc2_haplotypes()[1],
     peptide_length = 13,
-    percentile = 0.05
+    percentile = 0.05,
+    ic50_prediction_tool = "mhcnuggetsr"
   )
   # Results from verbose output:
   # Table: peptide length: 75, epitope length: 9, n fragments: 67,
@@ -148,43 +154,3 @@ test_that("use, NetMHC2pan, MHC-II, peptide length 13", {
   expect_equal(63, t$n_spots)
   expect_equal(46, t$n_spots_tmh)
 })
-
-
-test_that("profiling", {
-  if (!pureseqtmr::is_pureseqtm_installed()) return()
-  if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
-  if (!netmhc2pan::is_netmhc2pan_installed()) return()
-  return()
-
-  peptide <- "MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV" # nolint indeed long
-  profvis::profvis({
-    predict_counts(
-      protein_sequence = protein_sequence,
-      haplotype = get_mhc1_haplotypes()[1],
-      peptide_length = 10,
-      percentile = 0.05
-    )
-    predict_counts(
-      protein_sequence = protein_sequence,
-      haplotype = get_mhc1_haplotypes()[1],
-      peptide_length = 10,
-      percentile = 0.05,
-      ic50_prediction_tool = "EpitopePrediction"
-    )
-  })
-  profvis::profvis({
-    predict_counts(
-      protein_sequence = protein_sequence,
-      haplotype = get_mhc1_haplotypes()[2],
-      peptide_length = 13,
-      percentile = 0.05
-    )
-    predict_counts(
-      protein_sequence = protein_sequence,
-      haplotype = get_mhc1_haplotypes()[2],
-      peptide_length = 13,
-      percentile = 0.05,
-      ic50_prediction_tool = "netmhc2pan"
-    )
-  })
-})

tests/testthat/test-predict_counts_per_proteome.R

@@ -1,4 +1,5 @@
 test_that("MHCnuggetsr, peptide length 9", {
+  if (!pureseqtmr::is_on_travis()) return()
   if (!pureseqtmr::is_pureseqtm_installed()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
   protein_sequences <- c(
@@ -9,7 +10,8 @@ test_that("MHCnuggetsr, peptide length 9", {
     protein_sequences = protein_sequences,
     haplotype = get_mhc1_haplotypes()[1],
     peptide_length = 9,
-    percentile = 0.05
+    percentile = 0.05,
+   ic50_prediction_tool = "mhcnuggetsr"
   )
   expect_true(tibble::is_tibble(t))
   expect_equal(nrow(t), length(protein_sequences))
@@ -20,6 +22,7 @@ test_that("MHCnuggetsr, peptide length 9", {
 })
 
 test_that("MHCnuggetsr, peptide length 10", {
+  if (!pureseqtmr::is_on_travis()) return()
   if (!pureseqtmr::is_pureseqtm_installed()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
@@ -31,7 +34,8 @@ test_that("MHCnuggetsr, peptide length 10", {
     protein_sequences = protein_sequences,
     haplotype = get_mhc1_haplotypes()[1],
     peptide_length = 10,
-    percentile = 0.05
+    percentile = 0.05,
+   ic50_prediction_tool = "mhcnuggetsr"
   )
   expect_true(tibble::is_tibble(t))
   expect_equal(nrow(t), length(protein_sequences))
@@ -42,6 +46,7 @@ test_that("MHCnuggetsr, peptide length 10", {
 })
 
 test_that("MHCnuggetsr, MHC-II, peptide length 13", {
+  if (!pureseqtmr::is_on_travis()) return()
   if (!pureseqtmr::is_pureseqtm_installed()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
@@ -53,7 +58,8 @@ test_that("MHCnuggetsr, MHC-II, peptide length 13", {
     protein_sequences = protein_sequences,
     haplotype = get_mhc2_haplotypes()[1],
     peptide_length = 13,
-    percentile = 0.05
+    percentile = 0.05,
+   ic50_prediction_tool = "mhcnuggetsr"
   )
   expect_true(tibble::is_tibble(t))
   expect_equal(nrow(t), length(protein_sequences))
@@ -64,6 +70,7 @@ test_that("MHCnuggetsr, MHC-II, peptide length 13", {
 })
 
 test_that("MHCnuggetsr on short sequence", {
+  if (!pureseqtmr::is_on_travis()) return()
   if (!pureseqtmr::is_pureseqtm_installed()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
@@ -75,7 +82,8 @@ test_that("MHCnuggetsr on short sequence", {
     protein_sequences = protein_sequences,
     haplotype = get_mhc2_haplotypes()[1],
     peptide_length = 13,
-    percentile = 0.05
+    percentile = 0.05,
+   ic50_prediction_tool = "mhcnuggetsr"
   )
   expect_true(tibble::is_tibble(t))
   expect_equal(nrow(t), length(protein_sequences))

tests/testthat/test-predict_ic50s.R

@@ -1,5 +1,5 @@
 test_that("mhcnuggets", {
-
+  if (!pureseqtmr::is_on_travis()) return()
   if (!mhcnuggetsr::is_mhcnuggets_installed()) return()
 
   expect_silent(