-## read.GenBank.R (2007-06-27)
+## read.GenBank.R (2010-07-22)
## Read DNA Sequences from GenBank via Internet
-## Copyright 2002-2007 Emmanuel Paradis
+## Copyright 2002-2010 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
-read.GenBank <- function(access.nb, seq.names = access.nb,
- species.names = TRUE, as.character = FALSE)
+read.GenBank <-
+ function(access.nb, seq.names = access.nb, species.names = TRUE,
+ gene.names = FALSE, as.character = FALSE)
{
N <- length(access.nb)
## If there are more than 400 sequences, we need to break down the
}
FI <- grep("^ {0,}ORIGIN", X) + 1
LA <- which(X == "//") - 1
- obj <- list()
- length(obj) <- N
+ obj <- vector("list", N)
for (i in 1:N) {
## remove all spaces and digits
tmp <- gsub("[[:digit:] ]", "", X[FI[i]:LA[i]])
tmp <- character(N)
sp <- grep("ORGANISM", X)
for (i in 1:N)
- tmp[i] <- unlist(strsplit(X[sp[i]], " +ORGANISM +"))[2]
+ tmp[i] <- unlist(strsplit(X[sp[i]], " +ORGANISM +"))[2]
attr(obj, "species") <- gsub(" ", "_", tmp)
}
+ if (gene.names) {
+ tmp <- character(N)
+ sp <- grep(" +gene +<", X)
+ for (i in 1:N)
+ tmp[i] <- unlist(strsplit(X[sp[i + 1L]], " +/gene=\""))[2]
+ attr(obj, "gene") <- gsub("\"$", "", tmp)
+ }
obj
}