'Remove part of string after "."

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?

Solution 1:^[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"

Solution 2:^[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"

Solution 3:^[3]

You could do:

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

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

Solution 4:^[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"

Solution 5:^[5]

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:^[6]

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"

Sources

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Source: Stack Overflow

Solution	Source
Solution 1	Hansi
Solution 2	zx8754
Solution 3	johannes
Solution 4	akrun
Solution 5	benson23
Solution 6	user438383

'Remove part of string after "."

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