###############################################
# I run the following attachd code lines 
# But I kept getting error message like this:
###############################################

# when i is: 849 time is: Sun May 23 20:54:35 2010 
# when i is: 850 time is: Sun May 23 20:54:35 2010 
# Error in assign(".Method", method, envir = envir) : 
#   formal argument "envir" matched by multiple actual arguments
# Error in shift(restrict(nir, start = solved_start, end = solved_end),  : 
#   error in evaluating the argument 'x' in selecting a method for function 'shift'

# when i is: 1002 time is: Sun May 23 20:55:37 2010 
# when i is: 1003 time is: Sun May 23 20:55:37 2010 
# Error in assign(".target", method@target, envir = envir) : 
#   formal argument "envir" matched by multiple actual arguments
# Error in shift(restrict(nir, start = solved_start, end = solved_end),  : 
#  error in evaluating the argument 'x' in selecting a method for function 'shift'



###################################################################
#
#   The following is my code: 
# 
####################################################################

library("ShortRead")
library("Biostrings")
library("IRanges")
library("BSgenome")
library("rtracklayer")
library("biomaRt")
library("BSgenome.Hsapiens.UCSC.hg18")

get.rev.fasta<-function( chr = Hsapiens$chrX, chr.name="chrX" )
{
   # This funciton is used to get all bases for one chromosome and then reverse it to 
   # create a reversed fasta file. I will get the complement later

   options(digits=16)                 # We need to set up this, otherwise, num.line will just be an integer 
   num.line = floor(length(chr)/50)   # this gives the total number of lines, note, here we need to use floor 
   reminder = length(chr)%%50         # this gives the number of bases in the last line 

   LL<-length(chr)
 
   fasta.list<-as.character( rep(NA, num.line + 2 ) )
   fasta.list[1]<-paste(">", chr.name, sep="")    # This is the first line (e.g., ">chr1") in a fastq file. 

   for ( i in 1:num.line )
   {     # if (i%%5000==0) { cat("when i is:", i, "time is:", date(), "\n") }
         cat("when i is:", i, "time is:", date(), "\n") 

         start.1 = LL-i*50 +1 ; end.1 = LL-(i-1)*50
         xx<-getSeq(Hsapiens, paste(chr.name), start= start.1, end=end.1, strand="+")
         xx.1<-strsplit(xx, "")                    # split  string to a vector
         xx.2<-lapply(xx.1, rev)                   # reverse it 
         xx.3<-sapply(xx.2, paste, collapse="")    # convert vector to string 
         # class(xx.3)   # this is a chracter 
         fasta.list[i+1]<-xx.3
   }
  
    xx<-getSeq(Hsapiens, paste(chr.name), start=1 , end= reminder, strand="+")
    xx.1<-strsplit(xx, "")                   # split  string to a vector
    xx.2<-lapply(xx.1, rev)                  # reverse it 
    xx.3<-sapply(xx.2, paste, collapse="")   # convert vector to string 
    fasta.list[num.line + 1 ]<-xx.3          # This is the last line in the reverse fasta files. 

   return(fasta.list)
}
  
get.rev.fasta( chr = Hsapiens$chrX, chr.name="chrX" )