Subsetting a string based on pre- and suffix

Question

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)

score 2 · Answer 1 · answered Jan 28 '14 at 13:55

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.

score 2 · Answer 2 · answered Jan 28 '14 at 14:59

2

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

answered Jan 28 '14 at 14:59

Sven Hohenstein

80,497
17
145
168

Impressive! Thank you. – user3236594 Jan 28 '14 at 15:01

score 0 · Accepted Answer · answered Jan 28 '14 at 13:54

0

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

answered Jan 28 '14 at 13:54

Prasanna Nandakumar

4,295
34
63

Thank you! My final code is: test <- gsub(".*_.*_(.*)_.*", "\\1", x$names). This is the vector a want. – user3236594 Jan 28 '14 at 14:05

Subsetting a string based on pre- and suffix

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