CODEWITHSUNDEEP
rregexstring
Lisann
Lisann

Reputation: 5855

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?

Upvotes: 118

Views: 239336

Answers (6)

benson23
benson23

Reputation: 19097

We can use 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"

Upvotes: 5

user438383
user438383

Reputation: 6206

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"

Upvotes: 2

akrun
akrun

Reputation: 887008

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"

Upvotes: 11

zx8754
zx8754

Reputation: 56054

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"

Upvotes: 18

Hansi
Hansi

Reputation: 2634

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"

Upvotes: 164

johannes
johannes

Reputation: 14433

You could do:

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

or

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

Upvotes: 12

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