Added error handling to multiple functions in R/assign_job_queue.R, R/blastWrappers.R

R/blastWrappers.R

@@ -18,25 +18,56 @@
 #'
 #' @examples
 run_deltablast <- function(deltablast_path, db_search_path,
-    db = "refseq", query, evalue = "1e-5",
-    out, num_alignments, num_threads = 1) {
-    start <- Sys.time()
+                           db = "refseq", query, evalue = "1e-5",
+                           out, num_alignments, num_threads = 1) {
 
+  # Argument validation
+  if (!file.exists(deltablast_path)) {
+    stop("The DELTABLAST executable path is invalid: ", deltablast_path)
+  }
+  if (!dir.exists(db_search_path)) {
+    stop("The database search path is invalid: ", db_search_path)
+  }
+  if (!file.exists(query)) {
+    stop("The query file path is invalid: ", query)
+  }
+  if (!is.numeric(as.numeric(evalue)) || as.numeric(evalue) <= 0) {
+    stop("The evalue must be a positive number: ", evalue)
+  }
+  if (!is.numeric(num_alignments) || num_alignments <= 0) {
+    stop("The number of alignments must be a 
+         positive integer: ", num_alignments)
+  }
+  if (!is.numeric(num_threads) || num_threads <= 0) {
+    stop("The number of threads must be a positive integer: ", num_threads)
+  }
+
+  start <- Sys.time()
+
+  tryCatch({
     system(paste0("export BLASTDB=/", db_search_path))
 
     system2(
-        command = deltablast_path,
-        args = c(
-            "-db", db,
-            "-query", query,
-            "-evalue", evalue,
-            "-out", out,
-            "-num_threads", num_threads,
-            "-num_alignments", num_alignments
-            #   ,"-outfmt", outfmt
-        )
+      command = deltablast_path,
+      args = c(
+        "-db", db,
+        "-query", query,
+        "-evalue", evalue,
+        "-out", out,
+        "-num_threads", num_threads,
+        "-num_alignments", num_alignments
+        #   ,"-outfmt", outfmt
+      )
     )
     print(Sys.time() - start)
+  }, error = function(e) {
+    message(paste("Error in run_deltablast: ", e))
+  }, warning = function(w) {
+    message(paste("Warning in run_deltablast: ", w))
+  }, finally = {
+    message("run_deltablast completed")
+  })
+
 }
 
 
@@ -55,20 +86,48 @@ run_deltablast <- function(deltablast_path, db_search_path,
 #'
 #' @examples
 run_rpsblast <- function(rpsblast_path, db_search_path,
-    db = "refseq", query, evalue = "1e-5",
-    out, num_threads = 1) {
-    start <- Sys.time()
+                         db = "refseq", query, evalue = "1e-5",
+                         out, num_threads = 1) {
+  # Argument validation
+  if (!file.exists(rpsblast_path)) {
+    stop("The RPSBLAST executable path is invalid: ", rpsblast_path)
+  }
+  if (!dir.exists(db_search_path)) {
+    stop("The database search path is invalid: ", db_search_path)
+  }
+  if (!file.exists(query)) {
+    stop("The query file path is invalid: ", query)
+  }
+  if (!is.numeric(as.numeric(evalue)) || as.numeric(evalue) <= 0) {
+    stop("The evalue must be a positive number: ", evalue)
+  }
+  if (!is.numeric(num_threads) || num_threads <= 0) {
+    stop("The number of threads must be a positive integer: ", num_threads)
+  }
+
+  start <- Sys.time()
+
+  tryCatch({
+
     system(paste0("export BLASTDB=/", db_search_path))
+
     system2(
-        command = rpsblast_path,
-        args = c(
-            "-db", db,
-            "-query", query,
-            "-evalue", evalue,
-            "-out", out,
-            "-num_threads", num_threads
-            #                  , "-outfmt", outfmt
-        )
+      command = rpsblast_path,
+      args = c(
+        "-db", db,
+        "-query", query,
+        "-evalue", evalue,
+        "-out", out,
+        "-num_threads", num_threads
+      )
     )
     print(Sys.time() - start)
+  }, error = function(e) {
+    message(paste("Error in run_rpsblast: ", e))
+  }, warning = function(w) {
+    message(paste("Warning in run_rpsblast: ", w))
+  }, finally = {
+    message("run_rpsblast completed")
+  })
+
 }

R/clean_clust_file.R

@@ -55,9 +55,9 @@
 #'
 #' @examples
 #' \dontrun{
-#' clean_clust_file("data/pspa.op_ins_cls", writepath = NULL, query = "pspa")
+#' cleanClusterFile("data/pspa.op_ins_cls", writepath = NULL, query = "pspa")
 #' }
-clean_clust_file <- function(path, writepath = NULL, query) {
+cleanClusterFile <- function(path, writepath = NULL, query) {
     # ?? does the following line need to be changed to read_lines()?
     prot <- read_tsv(path, col_names = F)
 

R/create_lineage_lookup.R

@@ -101,7 +101,7 @@ create_lineage_lookup <- function(lineage_file = here("data/rankedlineage.dmp"),
 
 
 
-#' CreateLineageLookup <- function(assembly_path, updateAssembly = FALSE, file_type = "tsv")
+#' create_lineage_lookup <- function(assembly_path, updateAssembly = FALSE, file_type = "tsv")
 #' {
 #'   #' Create a look up table that goes from GCA_ID, to TaxID, to Lineage
 #'   #' @author Samuel Chen

R/msa.R

@@ -197,21 +197,21 @@ msa_pdf <- function(fasta_path, out_path = NULL,
 #'
 #' @examples
 generate_msa <- function(fa_file = "", outfile = "") {
-    prot_aa <- readAAStringSet(
-        path = fa_file,
-        format = "fasta"
-    )
-    prot_aa
+  prot_aa <- readAAStringSet(
+    fa_file,
+    format = "fasta"
+  )
+  prot_aa
 
-    ## Install kalign ?rMSA_INSTALL
-    ## Messed up! Reimplement from kalign.R
-    ## https://github.com/mhahsler/rMSA/blob/master/R/kalign.R
+  ## Install kalign ?rMSA_INSTALL
+  ## Messed up! Reimplement from kalign.R
+  ## https://github.com/mhahsler/rMSA/blob/master/R/kalign.R
 
-    # source("scripts/c2r.R")
+  # source("scripts/c2r.R")
 
-    ## align the sequences
-    al <- kalign(prot_aa) # !! won't work!
-    al
+  ## align the sequences
+  al <- kalign(prot_aa) # !! won't work!
+  al
 }
 
 ############################