Adding conditional statements to all functions using reticulate

BorchLab · Dec 31, 2024 · 48f1be3 · 48f1be3
1 parent 1ab0abb
commit 48f1be3
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Showing 12 changed files with 175 additions and 164 deletions.
diff --git a/R/onehotEncoder.R b/R/onehotEncoder.R
@@ -9,9 +9,11 @@
 #'                                    number.of.sequences = 100,
 #'                                    min.length = 8,
 #'                                    max.length = 16)
-#'                           
+#'                                    
+#' if(reticulate::py_module_available("numpy")) {                            
 #' sequence.matrix <- onehotEncoder(new.sequences, 
 #'                                  convert.to.matrix = TRUE)
+#' }
 #'                         
 #' @param input.sequences The amino acid or nucleotide sequences to use
 #' @param max.length Additional length to pad, NULL will pad sequences 

diff --git a/R/propertyEncoder.R b/R/propertyEncoder.R
@@ -10,10 +10,12 @@
 #'                                    number.of.sequences = 100,
 #'                                    min.length = 8,
 #'                                    max.length = 16)
-#'                           
+#'                                    
+#' if(reticulate::py_module_available("numpy")) {                            
 #' sequence.matrix <- propertyEncoder(new.sequences, 
 #'                                    method.to.use = "VHSE",
 #'                                    convert.to.matrix = TRUE)
+#' }
 #'                         
 #' @param input.sequences The amino acid sequences to use
 #' @param max.length Additional length to pad, NULL will pad sequences 

diff --git a/R/sequenceDecoder.R b/R/sequenceDecoder.R
@@ -9,12 +9,13 @@
 #'                                    number.of.sequences = 100,
 #'                                    min.length = 8,
 #'                                    max.length = 16)
-#'                           
+#' if(reticulate::py_module_available("numpy")) {                         
 #' sequence.matrix <- onehotEncoder(new.sequences, 
 #'                                  convert.to.matrix = TRUE)
 #'                                  
 #' decoded.sequences <- sequenceDecoder(sequence.matrix,
 #'                                      padding.symbol = ".")
+#' }
 #' 
 #' @param sequence.matrix The encoded sequences to decode in an array or matrix
 #' @param encoder The method to prepare the sequencing information - 

diff --git a/R/variationalSequences.R b/R/variationalSequences.R
@@ -4,19 +4,19 @@
 #' autoencoder (VAE) and perturbation of the probability distributions.
 #' 
 #' @examples
-#' \dontrun{
 #' sequences <- generateSequences(prefix.motif = "CAS",
 #'                                suffix.motif = "YF",
 #'                                number.of.sequences = 100,
 #'                                min.length = 8,
 #'                                max.length = 16)
-#'                                 
+#' 
+#' if(reticulate::py_module_available("keras")) {                                 
 #' new.sequences <- variationalSequences(sequences, 
 #'                                       encoder = "onehotEncoder",
 #'                                       encoder.hidden.dim = c(256, 128),
 #'                                       latent.dim = 16,
 #'                                       batch.size = 16)
-#' } 
+#'}
 #' 
 #' @param input.sequences The amino acid or nucleotide sequences to use
 #' @param encoder.function The method to prepare the sequencing information - 

diff --git a/man/onehotEncoder.Rd b/man/onehotEncoder.Rd
diff --git a/man/propertyEncoder.Rd b/man/propertyEncoder.Rd
diff --git a/man/sequenceDecoder.Rd b/man/sequenceDecoder.Rd
diff --git a/man/variationalSequences.Rd b/man/variationalSequences.Rd
diff --git a/tests/testthat/test-onehotEncoder.R b/tests/testthat/test-onehotEncoder.R
@@ -1,56 +1,56 @@
 # test script for onehotEncoder.R - testcases are NOT comprehensive!
 
 test_that("onehotEncoder works", {
-  
+
   sequences <- getdata("generateSequences", "generateSequences_T1")
-
-  ohe.default <- onehotEncoder(sequences)
-
-  expect_equal(
-    ohe.default,
-    getdata("ohe.encoder", "onehotEncoder_matrix")
-  )
-
-  ohe.2mer <- onehotEncoder(sequences, 
-                              motif.length = 2)
-  expect_equal(
-    ohe.2mer,
-    getdata("ohe.encoder", "onehotEncoder_2mer.matrix")
-  )
-
-  ohe.padded <- onehotEncoder(sequences,
-                                max.length = 40)
-
-  expect_equal(
-    ohe.padded,
-    getdata("ohe.encoder", "onehotEncoder_padded.matrix")
-  )
-
-  ohe.array <- onehotEncoder(sequences,
-                               convert.to.matrix = FALSE)
-
-  expect_equal(
-    ohe.array,
-    getdata("ohe.encoder", "onehotEncoder_array")
-  )
-
-  ohe.padded.array <- onehotEncoder(sequences,
-                               max.length = 40,
-                               convert.to.matrix = FALSE)
-
-  expect_equal(
-    ohe.padded.array,
-    getdata("ohe.encoder", "onehotEncoder_padded.array")
-  )
-
-  nt.sequences <- getdata("generateSequences", "generateSequences_T2")
-
-  ohe.nt <- onehotEncoder(nt.sequences,
-                            sequence.dictionary = c("A", "C", "T", "G"))
-
-  expect_equal(
-    ohe.nt,
-    getdata("ohe.encoder", "onehotEncoder_nucleotide.matrix")
-  )
-
+  if(reticulate::py_module_available("numpy")) {
+    ohe.default <- onehotEncoder(sequences)
+    
+    expect_equal(
+      ohe.default,
+      getdata("ohe.encoder", "onehotEncoder_matrix")
+    )
+    
+    ohe.2mer <- onehotEncoder(sequences, 
+                                motif.length = 2)
+    expect_equal(
+      ohe.2mer,
+      getdata("ohe.encoder", "onehotEncoder_2mer.matrix")
+    )
+    
+    ohe.padded <- onehotEncoder(sequences,
+                                  max.length = 40)
+    
+    expect_equal(
+      ohe.padded,
+      getdata("ohe.encoder", "onehotEncoder_padded.matrix")
+    )
+    
+    ohe.array <- onehotEncoder(sequences,
+                                 convert.to.matrix = FALSE)
+    
+    expect_equal(
+      ohe.array,
+      getdata("ohe.encoder", "onehotEncoder_array")
+    )
+    
+    ohe.padded.array <- onehotEncoder(sequences,
+                                 max.length = 40,
+                                 convert.to.matrix = FALSE)
+    
+    expect_equal(
+      ohe.padded.array,
+      getdata("ohe.encoder", "onehotEncoder_padded.array")
+    )
+    
+    nt.sequences <- getdata("generateSequences", "generateSequences_T2")
+    
+    ohe.nt <- onehotEncoder(nt.sequences,
+                              sequence.dictionary = c("A", "C", "T", "G"))
+    
+    expect_equal(
+      ohe.nt,
+      getdata("ohe.encoder", "onehotEncoder_nucleotide.matrix")
+    )
+  }
 })
diff --git a/tests/testthat/test-propertyEncoder.R b/tests/testthat/test-propertyEncoder.R
@@ -3,75 +3,75 @@
 test_that("propertyEncoder works", {
 
   sequences <- getdata("generateSequences", "generateSequences_T1")
-
-  #Return Matrix
-  af.matrix <- propertyEncoder(sequences,
-                                method.to.use = "atchleyFactors",
-                                convert.to.matrix = TRUE)
-
-  expect_equal(
-    af.matrix,
-    getdata("propertyEncoder", "propertyEncoder_AtchleyFactors_matrix")
-  )
-
-  #Return Array
-  kf.array <- propertyEncoder(sequences,
-                               method.to.use = "kideraFactors",
-                               convert.to.matrix = FALSE)
-
-  expect_equal(
-    kf.array,
-    getdata("propertyEncoder", "propertyEncoder_KideraFactors_array")
-  )
-
-  #Padded Matrix
-  fasgai.matrix <- propertyEncoder(sequences,
-                                    max.length = 40,
-                                    method.to.use = "FASGAI",
-                                    convert.to.matrix = FALSE)
-
-  expect_equal(
-    fasgai.matrix,
-    getdata("propertyEncoder", "propertyEncoder_FASGAI_matrix")
-  )
-
-  #Padded Array
-  vhse.array <- propertyEncoder(sequences,
-                                 max.length = 40,
-                                 method.to.use = "VHSE",
+    if(reticulate::py_module_available("numpy")) {
+    #Return Matrix
+    af.matrix <- propertyEncoder(sequences,
+                                  method.to.use = "atchleyFactors",
+                                  convert.to.matrix = TRUE)
+
+    expect_equal(
+      af.matrix,
+      getdata("propertyEncoder", "propertyEncoder_AtchleyFactors_matrix")
+    )
+
+    #Return Array
+    kf.array <- propertyEncoder(sequences,
+                                 method.to.use = "kideraFactors",
                                  convert.to.matrix = FALSE)
-
-  expect_equal(
-    vhse.array,
-    getdata("propertyEncoder", "propertyEncoder_VSHE_array")
-  )
-
-  #Return Summary Matrix
-  median.matrix <- propertyEncoder(sequences,
-                                    method.to.use = "atchleyFactors",
-                                    summary.function = "median")
-
-  expect_equal(
-    median.matrix,
-    getdata("propertyEncoder", "propertyEncoder_AtchleyFactors_median.matrix")
-  )
-
-  #Return multiple properties
-  multi.matrix <- propertyEncoder(sequences,
-                                   method.to.use = c("atchleyFactors", "kideraFactors"))
-
-  expect_equal(
-    multi.matrix,
-    getdata("propertyEncoder", "propertyEncoder_multi_matrix")
-  )
-
-  multi.array <- propertyEncoder(sequences,
-                                  method.to.use = c("VHSE", "tScales"),
-                                  convert.to.matrix = FALSE)
-
-  expect_equal(
-    multi.array,
-    getdata("propertyEncoder", "propertyEncoder_multi_array")
-  )
-
+
+    expect_equal(
+      kf.array,
+      getdata("propertyEncoder", "propertyEncoder_KideraFactors_array")
+    )
+
+    #Padded Matrix
+    fasgai.matrix <- propertyEncoder(sequences,
+                                      max.length = 40,
+                                      method.to.use = "FASGAI",
+                                      convert.to.matrix = FALSE)
+
+    expect_equal(
+      fasgai.matrix,
+      getdata("propertyEncoder", "propertyEncoder_FASGAI_matrix")
+    )
+
+    #Padded Array
+    vhse.array <- propertyEncoder(sequences,
+                                   max.length = 40,
+                                   method.to.use = "VHSE",
+                                   convert.to.matrix = FALSE)
+
+    expect_equal(
+      vhse.array,
+      getdata("propertyEncoder", "propertyEncoder_VSHE_array")
+    )
+
+    #Return Summary Matrix
+    median.matrix <- propertyEncoder(sequences,
+                                      method.to.use = "atchleyFactors",
+                                      summary.function = "median")
+
+    expect_equal(
+      median.matrix,
+      getdata("propertyEncoder", "propertyEncoder_AtchleyFactors_median.matrix")
+    )
+
+    #Return multiple properties
+    multi.matrix <- propertyEncoder(sequences,
+                                     method.to.use = c("atchleyFactors", "kideraFactors"))
+
+    expect_equal(
+      multi.matrix,
+      getdata("propertyEncoder", "propertyEncoder_multi_matrix")
+    )
+
+    multi.array <- propertyEncoder(sequences,
+                                    method.to.use = c("VHSE", "tScales"),
+                                    convert.to.matrix = FALSE)
+
+    expect_equal(
+      multi.array,
+      getdata("propertyEncoder", "propertyEncoder_multi_array")
+    )
+  }
 })