I want to solve two shorten notation in R.
For Ade/i, I should get Ade, Adi
For Do(i)lfal, I should get Dolfal, Doilfal
I have this solution
b='Do(i)lferl'
gsub(pattern = '(\\w+)\\((\\w+)+\\)', replacement='\\1\\i,\\1\\2', x=b)
Can anyone help me to code this
If these values are part of a dataframe, you can do this:
df <- data.frame(
Nickname = c("Ade/i", "Do(i)lfal")
)
df$Nickname_new[1] <- paste0(sub("(?=.*/)(.*)/.*", "\\1", df$Nickname[1], perl = T), ",", paste0(unlist(str_split(df$Nickname[1], "\\w/")), collapse = ""))
df$Nickname_new[2] <- paste0(sub("(.*)(\\(.*\\))(.*)", "\\1\\3", df$Nickname[2]),",", sub("(.*)\\((\\w)\\)(.*)", "\\1\\2\\3\\4", df$Nickname[2]))
which gives you:
df
Nickname Nickname_new
1 Ade/i Ade,Adi
2 Do(i)lfal Dolfal,Doilfal
EDIT:
Just in case the whole thing is not part of a dataframe but an atomic vector, you can do this:
x <- c("Ade/i", "Do(i)lfal")
c(paste0(sub("/.*", "", x[grepl("/", x)]), ", ", sub("./", "", x[grepl("/", x)])),
paste0(sub("(.*)\\((\\w)\\)(.*)", "\\1\\2\\3\\4", x[grepl("\\(", x)]), ", ", sub("\\(\\w\\)", "", x[grepl("\\(", x)])))
which gives you:
[1] "Ade, Adi" "Doilfal, Dolfal"
If there are values that you don't want to change, then this regex by #Wiktor will work (it works even with any scenario!):
x <- c("Ade/i", "Do(i)lfal", "Peter", "Mary")
gsub('(\\w*)\\((\\w+)\\)(\\w*)', '\\1\\2\\3, \\1\\3', gsub("(\\w*)(\\w)/(\\w)\\b", "\\1\\2, \\1\\3", x))
which gives you:
[1] "Ade, Adi" "Doilfal, Dolfal" "Peter" "Mary"
Related
I am sure there is a simple solution and I am just getting too frustrated to work through it but here is the issue, simplified:
I have a string, ex: AB^AB^AB^^BAAA^^BABA^
I want to replace the ^s (so, 7 characters in the string), but iterate through many variants and be able to retain them all as strings
for example:
replacement 1: CCDCDCD to get: ABCABCABDCBAAADCBABAD
replacement 2: DDDCCCD to get: ABDABDABDCBAAACCBABAD
I imagine strsplit is the way, and I would like to do it in a for loop, any help would be appreciated!
The positions of the "^" can be found using gregexpr, see tmp
x <- "AB^AB^AB^^BAAA^^BABA^"
y <- c("CCDCDCD", "DDDCCCD")
tmp <- gregexpr(pattern = "^", text = x, fixed = TRUE)
You can then split the 'replacements' character by character using strsplit, this gives a list. Finally, iterate over that list and replace the "^" with the characters from your replacements one after the other.
sapply(strsplit(y, split = ""), function(i) {
`regmatches<-`("AB^AB^AB^^BAAA^^BABA^", m = tmp, value = i)
})
Result
# [1] "ABCABCABCCBAAACCBABAC" "ABDABDABDDBAAADDBABAD"
You don't really need a for loop. You can strplit your string and pattern, and then replace the "^" with the vector.
str <- unlist(strsplit(str, ""))
pat <- unlist(strsplit("CCDCDCD", ""))
str[str == "^"] <- pat
paste(str, collapse = "")
# [1] "ABCABCABDCBAAADCBABAD"
An option is also with gsubfn
f1 <- Vectorize(function(str1, str2) {
p <- proto(fun = function(this, x) substr(str2, count, count))
gsubfn::gsubfn("\\^", p, str1)
})
-testing
> unname(f1(x, y))
[1] "ABCABCABDCBAAADCBABAD" "ABDABDABDCBAAACCBABAD"
data
x <- "AB^AB^AB^^BAAA^^BABA^"
y <- c("CCDCDCD", "DDDCCCD")
Given x <- "AB^AB^AB^^BAAA^^BABA^" and y <- c("CCDCDCD", "DDDCCCD"), we can try utf8ToInt + intToUtf8 + replace like below
sapply(
y,
function(s) {
intToUtf8(
replace(
u <- utf8ToInt(x),
u == utf8ToInt("^"),
utf8ToInt(s)
)
)
}
)
which gives
CCDCDCD DDDCCCD
"ABCABCABDCBAAADCBABAD" "ABDABDABDCBAAACCBABAD"
So, I am writing a function that, among many other things, is supposed to keep only the first sentence from each paragraph of a text and preserve the paragraph structure (i.e. each sentence is in its own line). Here is the code that I have so far:
text_shortener <- function(input_text) {
lapply(input_text, function(x)str_split(x, "\\.", simplify = T)[1])
first.sentences <- unlist(lapply(input_text, function(x)str_split(x, "\\.", simplify = T)[1]))
no.spaces <- gsub(pattern = "(?<=[\\s])\\s*|^\\s+|\\s+$", replacement = "", x = first.sentences, perl = TRUE)
stopwords <- c("the", "really", "truly", "very", "The", "Really", "Truly", "Very")
x <- unlist(strsplit(no.spaces, " "))
no.stopwords <- paste(x[!x %in% stopwords], collapse = " ")
final.text <- gsub(pattern = "(?<=\\w{5})\\w+", replacement = ".", x = no.stopwords, perl=TRUE)
return(final.text)
}
All of the functions are working as they should, but the one part I can't figure out is how to get the output to print onto separate lines. When I run the function with a vector of text (I was using some text from Moby Dick as a test), this is what I get:
> text_shortener(Moby_Dick)
[1] "Call me Ishma. It is a way I have of drivi. off splee., and regul. circu. This is my subst. for pisto. and ball"
What I want is for the output of this function to look like this:
[1] "Call me Ishma."
[2] "It is a way I have of drivi. off splee., and regul. circu."
[3] "This is my subst. for pisto. and ball"
I am relatively new to R and this giving me a real headache, so any help would be much appreciated! Thank you!
Looking at your output, it seems like splitting on a period followed by a capital letter if what you need.
You could accomplish that with strsplit() and split the string up like so:
strsplit("Call me Ishma. It is drivi. off splee., and regul. circu. This is my subst. for pisto.","\\. (?=[A-Z])", perl=T)
That finds instances where a period is followed by a space and a capital letter and splits the character up there.
Edit: You could add it to the end of your function like so:
text_shortener <- function(input_text) {
lapply(input_text, function(x)str_split(x, "\\.", simplify = T)[1])
first.sentences <- unlist(lapply(input_text, function(x)str_split(x, "\\.", simplify = T)[1]))
no.spaces <- gsub(pattern = "(?<=[\\s])\\s*|^\\s+|\\s+$", replacement = "", x = first.sentences, perl = TRUE)
stopwords <- c("the", "really", "truly", "very", "The", "Really", "Truly", "Very")
x <- unlist(strsplit(no.spaces, " "))
no.stopwords <- paste(x[!x %in% stopwords], collapse = " ")
trim.text <- gsub(pattern = "(?<=\\w{5})\\w+", replacement = ".", x = no.stopwords, perl=TRUE)
final.text <- strsplit(trim.text, "\\. (?=[A-Z])", perl=T)
return(final.text)
}
i think I have a simple question, but I did not get it. I have something like this:
df <- data.frame(identifier = c("9562231945200505501901190109-5405303
", "190109-8731478", "1901098260031", "
.9..43675190109-3690341", "-1103214010200000190109-8841419", "-190109-5232506-.08001234-111",
"190109-2018362-","51770217835901218103304190109-9339765
"), true_values = c("190109-5405303","190109-8731478","190109-8260031","190109-3690341","190109-8841419",
"190109-5232506","190109-2018362","190109-9339765"))
I used the following function and it almost worked, but I do not know how too avoid the last dash.
I tried str_replace and sth else, but it did not work.
You can try substr with paste after removing unwanted parts with gsub.
tt <- gsub("-\\..*", "", df$identifier)
tt <- gsub("[^0-9]", "", tt)
tt <- substring(tt, nchar(tt)-12)
paste0(substr(tt, 1, 6), "-", substring(tt, 7))
#[1] "190109-5405303" "190109-8731478" "190109-8260031" "190109-3690341"
#[5] "190109-8841419" "190109-5232506" "190109-2018362" "190109-9339765"
I have sequences that I want to reformat in R.
But R presents me the sequences with returns of lines (as can be seen with the "\n":
seqs <- ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAAC\nCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAA\nAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCT\nTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTT\nTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC---------\n-AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAA\nAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCAC\nCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAAT\nTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTAC\nCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTAT\nTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGT\nTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATC\nCTTTCTC-------------"
But I want to remove all the \nexcept the first one. I.e.:
[1] ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAACCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAAAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCTTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTTTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC----------AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAAAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCACCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAATTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTACCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTATTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGTTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATCCTTTCTC-------------"
If I do this, it removes all of the returns.
gsub(pattern = "\n",replacement = "", x = seqs)
This is not working:
sub("^(.*? \n .*?) \n .*", "\\1", seqs)
This gives me an error:
gsub(pattern = "${'\n'[*]:0:2}",replacement = "", x = seqs)
Error in gsub(pattern = "${'\n'[*]:0:2}", replacement = "", x = seqs) :
invalid regular expression '${'
'[*]:0:2}', reason 'Invalid contents of {}'
My sequences are variable:
">Whatever here before \n the sequence start \n the rest \n..."
The end result would be
">Whatever here before \n the sequence start the rest..."
Interestingly, the code below partially works for the test sentence, but not the sequence above:
seqss = ">Whatever here before \n the sequence start \n the rest \n..."
sub("^(.*? \n .*?) \n .*", "\\1", seqss)
[1] ">Whatever here before \n the sequence start"
Try it like this:
seqs <- ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAAC\nCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAA\nAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCT\nTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTT\nTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC---------\n-AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAA\nAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCAC\nCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAAT\nTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTAC\nCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTAT\nTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGT\nTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATC\nCTTTCTC-------------"
gsub(pattern = "(^.*?\\n)|\\n",replacement = "\\1", x = seqs, perl = TRUE)
regex101 demo
The idea of the regex
(^.*?\\n)|\\n
is to capture everything up to the first newline in a group to retain and put it back in the replacement.
A stringr approach that simply splits the string and combines the two parts back together.
seqs <- ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAAC\nCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAA\nAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCT\nTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTT\nTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC---------\n-AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAA\nAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCAC\nCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAAT\nTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTAC\nCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTAT\nTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGT\nTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATC\nCTTTCTC-------------"
library(stringr)
keep_first_newline <- function(string){
first_newline <- str_locate(string, "\\n")[1]
head <- str_sub(string, end = first_newline)
tail = string %>%
str_sub(start = first_newline + 1) %>%
str_remove_all("\\n")
out <- str_c(head, tail)
}
seqs %>%
keep_first_newline %>%
writeLines
#> >PRTRE213-13 Volkameria aculeatum matK
#> ------------------------------------------------------------------CCAACCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAAAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCTTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTTTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC----------AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAAAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCACCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAATTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTACCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTATTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGTTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATCCTTTCTC-------------
Created on 2018-06-29 by the reprex package (v0.2.0).
Using gsubfn we can do. Not any better than the regex in this case, but more easily extended if you want to keep the first n occurrences with n>1.
library(gsubfn)
p <- proto(fun = function(this, x) if(count > 1) '' else x)
out <- gsubfn('\n', p, seqs)
Same as accepted answer
out == gsub(pattern = "(^.*?\\n)|\\n",replacement = "\\1", x = seqs, perl = TRUE)
#[1] TRUE
I have a string variable containing alphabet[a-z], space[ ], and apostrophe['],eg. x <- "a'b c"
I want to replace apostrophe['] with blank[], and replace space[ ] with underscore[_].
x <- gsub("'", "", x)
x <- gsub(" ", "_", x)
It works absolutely, but when I have a lot of condition, the code becomes ugly. Therefore, I want to use chartr(), but chartr() can't deal with blank, eg.
x <- chartr("' ", "_", x)
#Error in chartr("' ", "_", "a'b c") : 'old' is longer than 'new'
Is there any way to solve this problem? thanks!
You can use gsubfn
library(gsubfn)
gsubfn(".", list("'" = "", " " = "_"), x)
# [1] "ab_c"
Similarly, we can also use mgsub which allows multiple replacement with multiple pattern to search
mgsub::mgsub(x, c("'", " "), c("", "_"))
#[1] "ab_c"
I am a fan of the syntax that the %<>% and %>% opperators from the magrittr package provide.
library(magrittr)
x <- "a'b c"
x %<>%
gsub("'", "", .) %>%
gsub(" ", "_", .)
x
##[1] "ab_c"
gusbfn is wonderful, but I like the chaining %>% allows.
I'd go with the quite fast function stri_replace_all_fixed from library(stringi):
library(stringi)
stri_replace_all_fixed("a'b c", pattern = c("'", " "), replacement = c("", "_"), vectorize_all = FALSE)
Here is a benchmark taking into account most of the other suggested solutions:
library(stringi)
library(microbenchmark)
library(gsubfn)
library(mgsub)
library(magrittr)
library(dplyr)
x_gsubfn <-
x_mgsub <-
x_nested_gsub <-
x_magrittr <-
x_stringi <- "a'b c"
microbenchmark("gsubfn" = { gsubfn(".", list("'" = "", " " = "_"), x_gsubfn) },
"mgsub" = { mgsub::mgsub(x_mgsub, c("'", " "), c("", "_")) },
"nested_gsub" = { gsub("Find", "Replace", gsub("Find","Replace", x_nested_gsub)) },
"magrittr" = { x_magrittr %<>% gsub("'", "", .) %>% gsub(" ", "_", .) },
"stringi" = { stri_replace_all_fixed(x_stringi, pattern = c("'", " "), replacement = c("", "_"), vectorize_all = FALSE) }
)
Unit: microseconds
expr min lq mean median uq max neval
gsubfn 458.217 482.3130 519.12820 513.3215 538.0100 715.371 100
mgsub 180.521 200.8650 221.20423 216.0730 231.6755 460.587 100
nested_gsub 14.615 15.9980 17.92178 17.7760 18.7630 40.687 100
magrittr 113.765 133.7125 148.48202 142.9950 153.0680 296.261 100
stringi 3.950 7.7030 8.41780 8.2960 9.0860 26.071 100
I know it is a bit old but it is hard to pass on an efficient base R solution. Just use the pipe:
test <- "abcegdfk461mnb"
test2 <- gsub("e|4|6","",test)
print(test2)
I think nested gsub will do the job.
gsub("Find","Replace",gsub("Find","Replace",X))
I would opt for a magrittr and/or dplyr solution, as well. However, I prefer not making a new copy of the object, especially if it is in a function and can be returned cheaply.
i.e.
return(
catInTheHat %>% gsub('Thing1', 'Thing2', .) %>% gsub('Red Fish', 'Blue
Fish', .)
)
...and so on.
gsub("\\s", "", chartr("' ", " _", x)) # Use whitespace and then remove it
Try this replace multi text character in column:
df$TYPE <- str_replace_all(df$TYPE, c("test" = "new_test", "G" = "N", "T" = "W"))
I use this function, which also allows omitting the argument for the replacement if the replacement is empty:
s=function(x,...,ignore.case=F,perl=F,fixed=F,useBytes=F){
a=match.call(expand.dots=F)$...
l=length(a)
for(i in seq(1,l,2))x=gsub(a[[i]],if(i==l)""else a[[i+1]],x,ignore.case=ignore.case,perl=perl,fixed=fixed,useBytes=useBytes)
x
}
> s("aa bb cc","aa","dd","bb")
[1] "dd cc"