regular expression string between two [ ] in R - regex

Question

I am stuck on regular expressions yet again but this time in R.
The problem I am facing is that I a vector I would like to extract a string between two [] for each row in the vector. However, sometimes I have cases where there is more than one series of [ ] in the whole statement and so I am recovering all strings in each row that is in the [ ]. In all cases I just need to recover the first instance of the string in the [ ] not the second or more instances. The example dataframe I have is:
comp541_c0_seq1 gi|356502740|ref|XP_003520174.1| PREDICTED: uncharacterized protein LOC100809655 [Glycine max]
comp5041_c0_seq1 gi|460370622|ref|XP_004231150.1| [Solanum lycopersicum] PREDICTED: uncharacterized protein LOC101250457 [Solanum lycopersicum]
The code i have been using that recovers the string and the index and makes a vector in the new dataframe are:
pattern <- "\\[\\w*\\s\\w*]"
match<- gregexpr(pattern, data$Description)
data$Species <- regmatches(data$Description, match)
the structure of the dataframe that I am using is:
data.frame': 67911 obs. of 6 variables:
$ Column1 : Factor w/ 67911 levels "comp100012_c0_seq1 ",..: 3344 8565 17875 18974 19059 19220 21429 29791 40214 48529 ...
$ Description : Factor w/ 26038 levels "0.0","1.13142e-173",..: NA NA NA NA NA NA NA NA 7970 NA ...
So the problem with my pattern match is that it return a vector (Species) where some of the rows have:
[Glycine max] # this is good
c("[Solanum lycopersicum]", "[Solanum lycopersicum]") # I only need one set returned
What I would like is:
[Glycine max]
[Solanum lycopersicum]
I have been trying every way I can with the regular expression. Would anyone know how to improve what I have to just extract the first instance of the string within [ ]?
Thanks in advance.

Answer 1

I think this example should be illuminating to your problems:
txt <- c("[Bracket text]","[Bracket text1] and [Bracket text2]","No brackets in here")
pattern <- "\\[\\w*\\s\\w*]"
mat <- regexpr(pattern,txt)
#[1] 1 1 -1
#attr(,"match.length")
#[1] 14 15 -1
txt[mat != -1] <- regmatches(txt, mat)
txt
#[1] "[Bracket text]" "[Bracket text1]" "No brackets in here"
Or if you want to do it all in one go and return NA values for non-matches, try:
ifelse(mat != -1, regmatches(txt,mat), NA)
#[1] "[Bracket text]" "[Bracket text1]" NA

Answer 2

Using the base-R facilities for string manipulation is just making life hard for yourself. Use rebus to create the regular expression, and stringi (or stringr) to get the matches.
library(rebus)
library(stringi)
txt <- c("[Bracket text]","[Bracket text1] and [Bracket text2]","No brackets in here") # thanks, thelatemail
pattern <- OPEN_BRACKET %R%
alnum(1, Inf) %R%
space(1, Inf) %R%
alnum(1, Inf) %R%
"]"
stri_extract_first_regex(txt, pattern)
## [1] "[Bracket text]" "[Bracket text1]" NA
I suspect that you probably don't want to keep those square brackets. Try this variant:
pattern <- OPEN_BRACKET %R%
capture(
alnum(1, Inf) %R%
space(1, Inf) %R%
alnum(1, Inf)
) %R%
"]"
stri_match_first_regex(txt, pattern)[, 2]
## [1] "Bracket text" "Bracket text1" NA