This script parses the (very useful but broken) list of CD markers and associated genes from Uniprot found at http://www.uniprot.org/docs/cdlist.txt

cdlist_parser.R

library(stringr)

screwed <- readLines(con='http://www.uniprot.org/docs/cdlist.txt')
screwed <- screwed[76:521]

parser <- c(0,8,21,29,37,55,1000000L) # use fixed length parsing

screwed <- lapply(screwed,function(scr) {
        sapply(seq(length(parser)-1),function(i) str_trim(substr(scr,parser[i]+1,parser[i+1])))
    }
)

screwed <- do.call(rbind,screwed)

colnames(screwed) <- c('CD_Number','SwissProt_Name','AC_Number','MIM_Number','Gene_Names','Synonyms')
head(screwed)