[Seqinr-commits] r2113 - pkg/R

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

Author: simonpenel
Date: 2021-05-18 14:29:27 +0200 (Tue, 18 May 2021)
New Revision: 2113

Modified:
   pkg/R/gbk2g2.R
Log:
replace ftp by https in gbk2g2.R

Modified: pkg/R/gbk2g2.R
===================================================================
--- pkg/R/gbk2g2.R	2021-03-17 08:49:16 UTC (rev 2112)
+++ pkg/R/gbk2g2.R	2021-05-18 12:29:27 UTC (rev 2113)
@@ -8,17 +8,17 @@
 #########################################################################
 
 gbk2g2 <- function(
-  gbkfile =  "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.gbk",
+  gbkfile =  "https://pbil.univ-lyon1.fr/datasets/seqinr/data/ct.gbk",
   g2.coord = "g2.coord")
 {
   input <- readLines(gbkfile)
-  
+
   outfile = file( description = g2.coord, open ="w")
   #
   # Keep lines with CDS flag:
   #
   input <- input[ substring(input,1,8) == "     CDS"]
-  
+
   #
   # Extract boudaries strings
   #
@@ -30,7 +30,7 @@
   }
   input <- sapply(input, get.boundaries)
   names(input) <- NULL
-  
+
   #
   # Look for 5' partial genes:
   #
@@ -37,7 +37,7 @@
   idx5p <- grep(">", input)
   if( length( idx5p != 0 ) )
     warning("5' partial genes encountered (no output):", idx5p)
-    
+
   #
   # Look for 3' partial genes:
   #
@@ -44,19 +44,19 @@
   idx3p <- grep("<", input)
   if( length( idx3p != 0 ) )
     warning("3' partial genes encountered (no output):", idx3p)
-    
+
   #
   # Look for join in features:
   #
   idxjoin <- grep("join", input)
   if( length( idxjoin != 0 ) )
-    warning("join encountered (no output):", idxjoin)  
-    
+    warning("join encountered (no output):", idxjoin)
+
   #
   # Define partials and join:
   #
   censored <-  c(idx5p, idx3p, idxjoin)
-  
+
   #
   # Extract boundaries:
   #
@@ -64,23 +64,22 @@
   {
     if( i %in% censored )
       next
-    
+
     tmp <- unlist( strsplit(input[i], split="\\.\\.") )
     if( length( grep("complement", input[i]) ) == 1 )
     {
       end <- as.integer( substring(tmp[1], first = 12 ) ) + as.integer(3)
       start <- as.integer( substring(tmp[2], first = 1, last = nchar(tmp[2]) - 1 ))
-      line <- sprintf(fmt = "%d %d %d", as.integer(i), start, end) 
+      line <- sprintf(fmt = "%d %d %d", as.integer(i), start, end)
     }
     else #direct strand
     {
       start <- as.integer(tmp[1])
       end   <- as.integer(tmp[2]) + as.integer(-3)
-      line <- sprintf(fmt = "%d %d %d", as.integer(i), start, end) 
+      line <- sprintf(fmt = "%d %d %d", as.integer(i), start, end)
     }
     writeLines( line, con = outfile )
   }
   close(outfile)
-  invisible(input)  
+  invisible(input)
 }
-