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########################################################################
#
# gb2fasta
#
# single entry genbank to fasta conversion
#
########################################################################
gb2fasta <- function(source.file, destination.file)
{
input <- readLines(source.file)
head <- input[1]
head <- unlist(strsplit(head, split=" "))
head <- head[nchar(head) > 0]
seqname <- head[2]
seqsize <- as.integer(head[3])
outheader <- sprintf(">%s %d bp", seqname, seqsize)
confile <- file(destination.file, open="w")
writeLines(outheader, confile)
#
# Look for sequence position:
#
debut <- which(substring(input,1,6) == "ORIGIN") + 1
if( length( debut ) > 1 )
stop("Multiple entries not yet implemented !")
fin <- which(substring(input,1,2) == "//") - 1
if( length( fin ) > 1 )
stop("Multiple entries not yet implemented !")
input <- input[debut:fin]
input <- sapply(input, function(x) {
return(paste(substr(x,11,20),substr(x,22,31),substr(x,33,42),substr(x,44,53),
substr(x,55,64),substr(x,66,75),sep="",collapse="")) } )
names(input)<-NULL
writeLines(input, confile )
close(confile)
}
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