Remove part of string after “.”

Question

I am working with NCBI Reference Sequence accession numbers like variable a:

a <- c("NM_020506.1","NM_020519.1","NM_001030297.2","NM_010281.2","NM_011419.3", "NM_053155.2")  

To get information from the biomart package I need to remove the .1, .2 etc. after the accession numbers. I normally do this with this code:

b <- sub("..*", "", a)

# [1] "" "" "" "" "" ""

But as you can see, this isn't the correct way for this variable. Can anyone help me with this?

Answer 1

You just need to escape the period:

a <- c("NM_020506.1","NM_020519.1","NM_001030297.2","NM_010281.2","NM_011419.3", "NM_053155.2")

gsub("\\..*","",a)
[1] "NM_020506"    "NM_020519"    "NM_001030297" "NM_010281"    "NM_011419"    "NM_053155" 

Answer 2

We can pretend they are filenames and remove extensions:

tools::file_path_sans_ext(a)
# [1] "NM_020506"    "NM_020519"    "NM_001030297" "NM_010281"    "NM_011419"    "NM_053155"

Answer 3

You could do:

sub("*\\.[0-9]", "", a)

or

library(stringr)
str_sub(a, start=1, end=-3)

Answer 4

If the string should be of fixed length, then substr from base R can be used. But, we can get the position of the . with regexpr and use that in substr

substr(a, 1, regexpr("\\.", a)-1)
#[1] "NM_020506"    "NM_020519"    "NM_001030297" "NM_010281"    "NM_011419"    "NM_053155"