CODEWITHSUNDEEP
regexrsubset
user3236594
user3236594

Reputation: 157

Subsetting a string based on pre- and suffix

I have a column with these type of names:

sp_O00168_PLM_HUMAM   
sp_Q8N1D5_CA158_HUMAN  
sp_Q15818_NPTX1_HUMAN  
tr_Q6FGH5_Q6FGH5_HUMAN  
sp_Q9UJ99_CAD22_HUMAN

I want to remove everything before, and including, the second _ and everything after, and including, the third _.

I do not which to remove based on number of characters, since this is not a fixed number.

The output should be: 

PLM  
CA158    
NPTX1  
Q6FGH5  
CAD22

I have played around with these, but don't quite get it right..
library(stringer)
str_sub(x,-6,-1)

Upvotes: 2

Views: 571

Answers (3)

Sven Hohenstein
Sven Hohenstein

Reputation: 81693

Another possible regular expression is this:

sub("^(?:.+_){2}(.+?)_.+", "\\1", vec)
# [1] "PLM"    "CA158"  "NPTX1"  "Q6FGH5" "CAD22"

where vec is your vector of strings.

A visual explanation:

Regular expression visualization

Upvotes: 2

Konrad Rudolph
Konrad Rudolph

Reputation: 545676

That’s not really a subset in programming terminology1, it’s a substring. In order to extract partial strings, you’d usually use regular expressions (pretty much regardless of language); in R, this is accessible via sub and other related functions:

pattern = '^.*_.*_([^_]*)_.*$'
result = sub(pattern, '\\1', strings)

1 Aside: taking a subset is, as the name says, a set operation, and sets are defined by having no duplicate elements and there’s no particular order to the elements. A string by contrast is a sequence which is a very different concept.

Upvotes: 2

Prasanna Nandakumar
Prasanna Nandakumar

Reputation: 4335

> gsub(".*_.*_(.*)_.*", "\\1", "sp_O00168_PLM_HUMAM") 
[1] "PLM"

Upvotes: 0

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