Remove part of string after "."
RR Problem Overview
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?
R Solutions
Solution 1 - R
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"
Solution 2 - R
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"
Solution 3 - R
You could do:
sub("*\\.[0-9]", "", a)
or
library(stringr)
str_sub(a, start=1, end=-3)
Solution 4 - R
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"
Solution 5 - R
We can a lookahead regex to extract the strings before ..
library(stringr)
str_extract(a, ".*(?=\\.)")
[1] "NM_020506" "NM_020519" "NM_001030297" "NM_010281"
[5] "NM_011419" "NM_053155"
Solution 6 - R
Another option is to use str_split from stringr:
library(stringr)
str_split(a, "\\.", simplify=T)[,1]
[1] "NM_020506" "NM_020519" "NM_001030297" "NM_010281" "NM_011419" "NM_053155"