I have a sequence like this in a list "MSGSRRKATPASRTRVGNYEMGRTLGEGSFAKVKYAKNTVTGDQAAIKILDREKVFRHKMVEQLKREISTMKLIKHPNVVEIIEVMASKTKIYIVLELVNGGELFDKIAQQGRLKEDEARRYFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDFGLSAFSRQVREDGLLHTACGTPNYVAPEVLSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYKRICKAEFSCPPWFSQGAKRVIKRILEPNPITRISIAELLEDEWFKKGYKPPSFDQDDEDITIDDVDAAFSNSKECLVTEKKEKPVSMNAFELISSSSEFSLENLFEKQAQLVKKETRFTSQRSASEIMSKMEETAKPLGFNVRKDNYKIKMKGDKSGRKGQLSVATEVFEVAPSLHVVELRKTGGDTLEFHKVCDSFYKNFSSGLKDVVWNTDAAAEEQKQ"
I would like to create a substring like wherever a "K" is present it needs to pull out 6 characters before and 6 characters after "K"
Ex : MSGSRRKATPASR , here -6..K..+6
for the whole sequence..I tried the substring function in R but we need to specify the start and end position. Here the positions are unknown
Thanks
.{6}K.{6}
Try this.This will give the desired result.
See demo.
http://regex101.com/r/dM0rS8/4
use this:
\w{7}(?<=K)\w{6}
this uses positive lookbehind to ensure that there are characters present before K.
demo here: http://regex101.com/r/pK3jK1/2
Using rex may make this type of task a little simpler.
x <- "MSGSRRKATPASRTRVGNYEMGRTLGEGSFAKVKYAKNTVTGDQAAIKILDREKVFRHKMVEQLKREISTMKLIKHPNVVEIIEVMASKTKIYIVLELVNGGELFDKIAQQGRLKEDEARRYFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDFGLSAFSRQVREDGLLHTACGTPNYVAPEVLSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYKRICKAEFSCPPWFSQGAKRVIKRILEPNPITRISIAELLEDEWFKKGYKPPSFDQDDEDITIDDVDAAFSNSKECLVTEKKEKPVSMNAFELISSSSEFSLENLFEKQAQLVKKETRFTSQRSASEIMSKMEETAKPLGFNVRKDNYKIKMKGDKSGRKGQLSVATEVFEVAPSLHVVELRKTGGDTLEFHKVCDSFYKNFSSGLKDVVWNTDAAAEEQKQ"
library(rex)
re_matches(x,
rex(
capture(name = "amino_acids",
n(any, 6),
"K",
n(any, 6)
)
),
global = TRUE)[[1]]
#> amino_acids
#>1 MSGSRRKATPASR
#>2 GEGSFAKVKYAKN
#>3 GDQAAIKILDREK
#>4 KMVEQLKREISTM
#>5 IEVMASKTKIYIV
#>6 GGELFDKIAQQGR
#>7 VYHRDLKPENLIL
#>8 DANGVLKVSDFGL
#>9 PEVLSDKGYDGAA
#>10 NLMTLYKRICKAE
#>11 WFSQGAKRVIKRI
#>12 LEDEWFKKGYKPP
#>13 AAFSNSKECLVTE
#>14 LENLFEKQAQLVK
#>15 ASEIMSKMEETAK
#>16 LGFNVRKDNYKIK
#>17 GDKSGRKGQLSVA
#>18 HVVELRKTGGDTL
#>19 VCDSFYKNFSSGL
However the above is greedy, each K will only appear in one result.
If you want to output an AA for each K
library(rex)
locs <- re_matches(x,
rex(
"K" %if_prev_is% n(any, 6) %if_next_is% n(any, 6)
),
global = TRUE, locations = TRUE)[[1]]
substring(x, locs$start - 6, locs$end + 6)
#> [1] "MSGSRRKATPASR" "GEGSFAKVKYAKN" "GSFAKVKYAKNTV" "AKVKYAKNTVTGD"
#> [5] "GDQAAIKILDREK" "KILDREKVFRHKM" "EKVFRHKMVEQLK" "KMVEQLKREISTM"
#> [9] "REISTMKLIKHPN" "STMKLIKHPNVVE" "IEVMASKTKIYIV" "VMASKTKIYIVLE"
#>[13] "GGELFDKIAQQGR" "AQQGRLKEDEARR" "VYHRDLKPENLIL" "DANGVLKVSDFGL"
#>[17] "PEVLSDKGYDGAA" "NLMTLYKRICKAE" "LYKRICKAEFSCP" "WFSQGAKRVIKRI"
#>[21] "GAKRVIKRILEPN" "LEDEWFKKGYKPP" "EDEWFKKGYKPPS" "WFKKGYKPPSFDQ"
#>[25] "AAFSNSKECLVTE" "ECLVTEKKEKPVS" "CLVTEKKEKPVSM" "VTEKKEKPVSMNA"
#>[29] "LENLFEKQAQLVK" "KQAQLVKKETRFT" "QAQLVKKETRFTS" "ASEIMSKMEETAK"
#>[33] "KMEETAKPLGFNV" "LGFNVRKDNYKIK" "VRKDNYKIKMKGD" "KDNYKIKMKGDKS"
#>[37] "NYKIKMKGDKSGR" "IKMKGDKSGRKGQ" "GDKSGRKGQLSVA" "HVVELRKTGGDTL"
#>[41] "DTLEFHKVCDSFY" "VCDSFYKNFSSGL" "NFSSGLKDVVWNT"
Related
I'd like to match everything between the first and last underscore. I use R.
What I have until now is this:
p.subject <- c('bla_bla', 'bla', 'bla_bla_bla', 'bla_bla_bla_bla')
sub('[^_]*_(.*)_[^_]*', x = p.subject, replacement = '\\1', perl = T)
Where 'bla' is any character except an underscore...
The result I'd like would be something like this:
c(NA, NA, bla, bla_bla)
I can't figure it out! Why does the first pattern match? It shouldn't because the pattern must have 2 underscores! Or do I have to use some kind of lookahead expression?
Your help is very welcome!
You can use gsub:
vec <- gsub("(^[^_]+)_?|_?([^_]+$)", "", p.subject)
vec <- ifelse(nchar(vec) == 0 , NA, vec)
vec
[1] NA NA "bla" "bla_bla"
Data:
dput(p.subject)
c("bla_bla", "bla", "bla_bla_bla", "bla_bla_bla_bla")
Here is another option using str_extract. We use regex lookarounds to extract the pattern between the first and the last occurrence of a specified character i.e. _.
library(stringr)
str_extract(p.subject, "(?<=[^_]{1,30}_).*(?=_[^_]+)")
#[1] NA NA "bla" "bla_bla"
NOTE: We didn't use any ifelse.
data
p.subject <- c('bla_bla', 'bla', 'bla_bla_bla', 'bla_bla_bla_bla')
I want to extract the 12 and the 0 from the test vector. Every time I try it would either give me 120 or 12:0
TestVector <- c("12:0")
gsub("\\b[:numeric:]*",replacement = "\\1", x = TestVector, fixed = F)
What can I use to extract the 12 and the 0. Can we just have one where I just extract the 12 so I can change it to extract the 0. Can we do this exclusively with gsub?
One option, which doesn't involve using explicit regular expressions, would be to use strsplit() and split the timestamp on the colon:
TestVector <- c("12:0")
parts <- unlist(strsplit(TestVector, ":")))
> parts[1]
[1] "12"
> parts[2]
[1] "0"
Try this
gsub("\\b(\\d+):(\\d+)\\b",replacement = "\\1 \\2", x = TestVector, fixed = F)
Regex Breakdown
\\b #Word boundary
(\\d+) #Find all digits before :
: #Match literally colon
(\\d+) #Find all digits after :
\\b #Word boundary
I think there is no named class as [:numeric:] in R till I know, but it has named class [[:digit:]]. You can use it as
gsub("\\b([[:digit:]]+):([[:digit:]]+)\\b",replacement = "\\1 \\2", x = TestVector)
As suggested by rawr, a much simpler and intuitive way to do it would be to just simply replace : with space
gsub(":",replacement = " ", x = TestVector, fixed = F)
This can be done using scan from base R
scan(text=TestVector, sep=":", what=numeric(), quiet=TRUE)
#[1] 12 0
or with str_extract
library(stringr)
str_extract_all(TestVector, "[^:]+")[[1]]
I'm still a little confused by regex syntax. Can you please help me with these patterns:
_A00_A1234B_
_A00_A12345B_
_A1_A12345_
my approaches so far:
vapply(strsplit(files, "[_.]"), function(files) files[nchar(files) == 7][1], character(1))
or
str_extract(str2, "[A-Z][0-9]{5}[A-Z]")
The expected outputs are
A1234B
A12345B
A12345
Thanks!
You can try
library(stringr)
str_extract(str2, "[A-Z][0-9]{4,5}[A-Z]?")
#[1] "A1234B" "A12345B" "A12345"
Here, the pattern looks for a capital letter [A-Z], followed by 4 or 5 digits [0-9]{4,5}, followed by a capital letter [A-Z] ?
Or you can use stringi which would be faster
library(stringi)
stri_extract(str2, regex="[A-Z][0-9]{4,5}[A-Z]?")
#[1] "A1234B" "A12345B" "A12345"
Or a base R option would be
regmatches(str2,regexpr('[A-Z][0-9]{4,5}[A-Z]?', str2))
#[1] "A1234B" "A12345B" "A12345"
data
str2 <- c('_A00_A1234B_', '_A00_A12345B_', '_A1_A12345_')
vec <- c("_A00_A1234B_", "_A00_A12345B_", "_A1_A12345_")
You can use sub and this regex:
sub(".*([A-Z]\\d{4,5}[A-Z]?).*", "\\1", vec)
# [1] "A1234B" "A12345B" "A12345"
Using rex to construct the regular expression may make it more understandable.
x <- c("_A00_A1234B_", "_A00_A12345B_", "_A1_A12345_")
# approach #1, assumes always is between the second underscores.
re_matches(x,
rex(
"_",
anything,
"_",
capture(anything),
"_"
)
)
#> 1
#> 1 A1234B
#> 2 A12345B
#> 3 A12345
# approach #2, assumes an alpha, followed by 4 or 5 digits with a possible trailing alpha.
re_matches(x,
rex(
capture(
alpha,
between(digit, 4, 5),
maybe(alpha)
)
)
)
#> 1
#> 1 A1234B
#> 2 A12345B
#> 3 A12345
You can do this without using a regular expression ...
x <- c('_A00_A1234B_', '_A00_A12345B_', '_A1_A12345_')
sapply(strsplit(x, '_', fixed=T), '[', 3)
# [1] "A1234B" "A12345B" "A12345"
If you insist on using a regular expression, the following will suffice.
regmatches(x, regexpr('[^_]+(?=_$)', x, perl=T))
string = "ABC3JFD456"
Suppose I have the above string, and I wish to find what the first digit in the string is and store its value. In this case, I would want to store the value 3 (since it's the first-occuring digit in the string). grepl("\\d", string) only returns a logical value, but does not tell me anything about where or what the first digit is. Which regular expression should I use to find the value of the first digit?
Base R
regmatches(string, regexpr("\\d", string))
## [1] "3"
Or using stringi
library(stringi)
stri_extract_first(string, regex = "\\d")
## [1] "3"
Or using stringr
library(stringr)
str_extract(string, "\\d")
## [1] "3"
1) sub Try sub with the indicated regular expression which takes the shortest string until a digit, a digit and then everything following and replaces it with the digit:
sub(".*?(\\d).*", "\\1", string)
giving:
[1] "3"
This also works if string is a vector of strings.
2) strapplyc It would also be possible to use strapplyc from gsubfn in which case an even simpler regular expression could be used:
strapplyc(string, "\\d", simplify = TRUE)[1]
giving the same or use this which gives the same answer again but also works if string is a vector of strings:
sapply(strapplyc(string, "\\d"), "[[", 1)
Get the locations of the digits
tmp <- gregexpr("[0-9]", string)
iloc <- unlist(tmp)[1]
Extract the first digit
as.numeric(substr(string,iloc,iloc))
Using regexpr is simpler
tmp<-regexpr("[0-9]",string)
if(tmp[[1]]>=0) {
iloc <- tmp[1]
num <- as.numeric(substr(string,iloc,iloc))
}
Using rex may make this type of task a little simpler.
string = c("ABC3JFD456", "ARST4DS324")
re_matches(string,
rex(
capture(name = "first_number", digit)
)
)
#> first_number
#> 1 3
#> 2 4
> which( sapply( strsplit(string, ""), grepl, patt="[[:digit:]]"))[1]
[1] 4
Or
> gregexpr("[[:digit:]]", string)[[1]][1]
[1] 4
So:
> splstr[[1]][ which( sapply( splstr, grepl, patt="[[:digit:]]"))[1] ]
[1] "3"
Note that a full result from a gregexpr call is a list, hence the need to extract its first element with "[[":
> gregexpr("[[:digit:]]", string)
[[1]]
[1] 4 8 9 10
attr(,"match.length")
[1] 1 1 1 1
attr(,"useBytes")
[1] TRUE
A gsub solution that is based on replacing the substrings preceding and following the first digit with the empty string:
gsub("^\\D*(?=\\d)|(?<=\\d).*", "", string, perl = TRUE)
# [1] "3"
A comment on my answer to this question which should give the desired result using strsplit does not, even though it seems to correctly match the first and last commas in a character vector. This can be proved using gregexpr and regmatches.
So why does strsplit split on each comma in this example, even though regmatches only returns two matches for the same regex?
# We would like to split on the first comma and
# the last comma (positions 4 and 13 in this string)
x <- "123,34,56,78,90"
# Splits on every comma. Must be wrong.
strsplit( x , '^\\w+\\K,|,(?=\\w+$)' , perl = TRUE )[[1]]
#[1] "123" "34" "56" "78" "90"
# Ok. Let's check the positions of matches for this regex
m <- gregexpr( '^\\w+\\K,|,(?=\\w+$)' , x , perl = TRUE )
# Matching positions are at
unlist(m)
[1] 4 13
# And extracting them...
regmatches( x , m )
[[1]]
[1] "," ","
Huh?! What is going on?
The theory of #Aprillion is exact, from R documentation:
The algorithm applied to each input string is
repeat {
if the string is empty
break.
if there is a match
add the string to the left of the match to the output.
remove the match and all to the left of it.
else
add the string to the output.
break.
}
In other words, at each iteration ^ will match the begining of a new string (without the precedent items.)
To simply illustrate this behavior:
> x <- "12345"
> strsplit( x , "^." , perl = TRUE )
[[1]]
[1] "" "" "" "" ""
Here, you can see the consequence of this behavior with a lookahead assertion as delimiter (Thanks to #JoshO'Brien for the link.)