[Seqinr-commits] r2127 - pkg/R

[noreply at r-forge.r-project.org]

Author: simonpenel
Date: 2021-05-25 13:40:28 +0200 (Tue, 25 May 2021)
New Revision: 2127

Modified:
   pkg/R/comp.R
Log:
Correction of comp function according to Dr. Haruo Suzuki

Modified: pkg/R/comp.R
===================================================================
--- pkg/R/comp.R	2021-05-25 11:35:20 UTC (rev 2126)
+++ pkg/R/comp.R	2021-05-25 11:40:28 UTC (rev 2127)
@@ -3,13 +3,13 @@
 ###########################################
 
 comp <- function(seq, forceToLower = TRUE, ambiguous = FALSE){
-  
+
   if(all(seq %in% LETTERS)){
   	  isUpper <- TRUE
   	} else {
   	  isUpper <- FALSE
   	}
-  	
+
   	seq <- tolower(seq)
 
   result <- as.vector(n2s((3-s2n(seq))))
@@ -16,7 +16,7 @@
   #
   # More work is required if ambiguous bases are taken into account
   #
-  
+
   if(ambiguous){
     result[which(seq == "b")] <- "v"
     result[which(seq == "d")] <- "h"
@@ -26,19 +26,18 @@
     result[which(seq == "s")] <- "s"
     result[which(seq == "v")] <- "b"
     result[which(seq == "w")] <- "w"
-    result[which(seq == "n")] <- "n"    
+    result[which(seq == "n")] <- "n"
     result[which(seq == "y")] <- "r"
     result[which(seq == "r")] <- "y"
   }
-  
-  # Checking for N in the sequence, thanks to Jeremy Shearman. 
-  
-  result[which(seq == "n")] <- "n"	
-  
-  
+
+  # Checking for N in the sequence, thanks to Jeremy Shearman.
+  # Now this is done only with ambigous option, thanks to Suzuki Haruo
+  # result[which(seq == "n")] <- "n"
+
+
   if(isUpper && !forceToLower){
   	  result <- toupper(result)
   	}
   return(result)
 }
-