add unit tests to cleanup.R

DESCRIPTION

@@ -82,4 +82,7 @@ Imports:
     XVector,
     yaml
 Suggests:
-    knitr
+    knitr,
+    testthat,
+    mockery,
+    readr

R/cleanup.R

@@ -160,9 +160,10 @@ removeEmptyRows <- function(prot, by_column = "DomArch") {
     prot <- prot %>%
         as_tibble() %>%
         # filter(grepl("\\*", {{by_column}})) %>%		  # Keep only rows with Query (*) for GenContext
-        filter(!grepl("^-$", {{ by_column }})) %>% # remove "-"
-        filter(!grepl("^NA$", {{ by_column }})) %>% # remove "NA"
-        filter(!grepl("^$", {{ by_column }})) # remove empty rows
+        filter(!grepl("^-$", .[[by_column]])) %>%   # remove "-"
+        filter(!grepl("^NA$", .[[by_column]])) %>%  # remove "NA"
+        filter(!grepl("^$", .[[by_column]])) %>%    # remove empty rows
+        filter(!grepl("^\\s*$", .[[by_column]]))     # remove rows with only spaces
 
     return(prot)
 }

R/fa2domain.R

@@ -22,6 +22,16 @@ runIPRScan <- function(
         # destPartition = "LocalQ",
         # destQoS = "shortjobs"
     ) {
+    # Validate inputs
+    if (is.null(filepath_fasta) || filepath_fasta == "") {
+        stop("filepath_fasta cannot be NULL or empty")
+    }
+    if (is.null(filepath_out) || filepath_out == "") {
+        stop("filepath_out cannot be NULL or empty")
+    }
+    if (!all(appl %in% c("Pfam", "Gene3D"))) {
+        stop("Invalid application specified")
+    }
     # construct interproscan command
     cmd_iprscan <- stringr::str_glue(
         "iprscan -i {filepath_fasta} -b {filepath_out} --cpu 4 -f TSV ",
@@ -283,7 +293,7 @@ getDomainsFromFA <- function(
                 if (verbose) {
                     msg <- stringr::str_glue(
                         "accession number: {header} had no domains for the ",
-                        "selected analyes: {paste(analysis, collapse = ',')}\n"
+                        "selected analyses: {paste(analysis, collapse = ',')}\n"
                     )
                     warning(msg)
                 }

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(MolEvolvR)
+
+test_check("MolEvolvR")