Merge pull request #99 from teddyCodex/issue-55-rename-functions

Refactor function names in R/blastWrapper.R
- fixes #55

NAMESPACE

@@ -79,8 +79,8 @@ export(renameFA)
 export(rename_fasta)
 export(replaceQuestionMarks)
 export(reverseOperonSeq)
-export(run_deltablast)
-export(run_rpsblast)
+export(runDeltaBlast)
+export(runRPSBlast)
 export(selectLongestDuplicate)
 export(sendJobStatusEmail)
 export(shortenLineage)

R/blastWrappers.R

@@ -17,12 +17,10 @@
 #' @export
 #'
 #' @examples
-run_deltablast <- function(deltablast_path, db_search_path,
-                           db = "refseq", query, evalue = "1e-5",
-                           out, num_alignments, num_threads = 1) {
-
-  start <- Sys.time()
-
+runDeltaBlast <- function(deltablast_path, db_search_path,
+    db = "refseq", query, evalue = "1e-5",
+    out, num_alignments, num_threads = 1) {
+    start <- Sys.time()
 
   system(paste0("export BLASTDB=/", db_search_path))
 
@@ -57,22 +55,21 @@ run_deltablast <- function(deltablast_path, db_search_path,
 #' @export
 #'
 #' @examples
-run_rpsblast <- function(rpsblast_path, db_search_path,
-                         db = "refseq", query, evalue = "1e-5",
-                         out, num_threads = 1) {
-
-  start <- Sys.time()
-  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
+runRPSBlast <- function(rpsblast_path, db_search_path,
+    db = "refseq", query, evalue = "1e-5",
+    out, num_threads = 1) {
+    start <- Sys.time()
+    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
+        )
     )
-  )
-  print(Sys.time() - start)
+    print(Sys.time() - start)
 }