Related
I am on the lookout for a gsub based function which would enable me to do combinatorial string replacement, so that if I would have an arbitrary number of string replacement rules
replrules=list("<x>"=c(3,5),"<ALK>"=c("hept","oct","non"),"<END>"=c("ane","ene"))
and a target string
string="<x>-methyl<ALK><END>"
it would give me a dataframe with the final string name and the substitutions that were made as in
name x ALK END
3-methylheptane 3 hept ane
5-methylheptane 5 hept ane
3-methyloctane 3 oct ane
5-methyloctane 5 ... ...
3-methylnonane 3
5-methylnonane 5
3-methylheptene 3
5-methylheptene 5
3-methyloctene 3
5-methyloctene 5
3-methylnonene 3
5-methylnonene 5
The target string would be of arbitrary structure, e.g. it could also be string="1-<ALK>anol" or each pattern could occur several times, as in string="<ALK>anedioic acid, di<ALK>yl ester"
What would be the most elegant way to do this kind of thing in R?
How about
d <- do.call(expand.grid, replrules)
d$name <- paste0(d$'<x>', "-", "methyl", d$'<ALK>', d$'<END>')
EDIT
This seems to work (substituting each of these into the strplit)
string = "<x>-methyl<ALK><END>"
string2 = "<x>-ethyl<ALK>acosane"
string3 = "1-<ALK>anol"
Using Richards regex
d <- do.call(expand.grid, list(replrules, stringsAsFactors=FALSE))
names(d) <- gsub("<|>","",names(d))
s <- strsplit(string3, "(<|>)", perl = TRUE)[[1]]
out <- list()
for(i in s) {
out[[i]] <- ifelse (i %in% names(d), d[i], i)
}
d$name <- do.call(paste0, unlist(out, recursive=F))
EDIT
This should work for repeat items
d <- do.call(expand.grid, list(replrules, stringsAsFactors=FALSE))
names(d) <- gsub("<|>","",names(d))
string4 = "<x>-methyl<ALK><END>oate<ALK>"
s <- strsplit(string4, "(<|>)", perl = TRUE)[[1]]
out <- list()
for(i in seq_along(s)) {
out[[i]] <- ifelse (s[i] %in% names(d), d[s[i]], s[i])
}
d$name <- do.call(paste0, unlist(out, recursive=F))
Well, I'm not exactly sure we can even produce a "correct" answer to your question, but hopefully this helps give you some ideas.
Okay, so in s, I just split the string where it might be of most importance. Then g gets the first value in each element of r. Then I constructed a data frame as an example. So then dat is a one row example of how it would look.
> (s <- strsplit(string, "(?<=l|\\>)", perl = TRUE)[[1]])
# [1] "<x>" "-methyl" "<ALK>" "<END>"
> g <- sapply(replrules, "[", 1)
> dat <- data.frame(name = paste(append(g, s[2], after = 1), collapse = ""))
> dat[2:4] <- g
> names(dat)[2:4] <- sapply(strsplit(names(g), "<|>"), "[", -1)
> dat
# name x ALK END
# 1 3-methylheptane 3 hept ane
Please bear with me, I come from a Python background and I am still learning string manipulation in R.
Ok, so lets say I have a string of length 100 with random A, B, C, or D letters:
> df<-c("ABCBDBDBCBABABDBCBCBDBDBCBDBACDBCCADCDBCDACDDCDACBCDACABACDACABBBCCCBDBDDCACDDACADDDDACCADACBCBDCACD")
> df
[1]"ABCBDBDBCBABABDBCBCBDBDBCBDBACDBCCADCDBCDACDDCDACBCDACABACDACABBBCCCBDBDDCACDDACADDDDACCADACBCBDCACD"
I would like to do the following two things:
1) Generate a '.txt' file that is comprised of 20-length subsections of the above string, each starting one letter after the previous with their own unique name on the line above it, like this:
NAME1
ABCBDBDBCBABABDBCBCB
NAME2
BCBDBDBCBABABDBCBCBD
NAME3
CBDBDBCBABABDBCBCBDB
NAME4
BDBDBCBABABDBCBCBDBD
... and so forth
2) Take that generated list and from it comprise another list that has the same exact substrings with the only difference being a change of one or two of the A, B, C, or Ds to another A, B, C, or D (any of those four letters only).
So, this:
NAME1
ABCBDBDBCBABABDBCBCB
Would become this:
NAME1.1
ABBBDBDBCBDBABDBCBCB
As you can see, the "C" in the third position became a "B" and the "A" in position 11 became a "D", with no implied relationship between those changed letters. Purely random.
I know this is a convoluted question, but like I said, I am still learning basic text and string manipulation in R.
Thanks in advance.
Create a text file of substrings
n <- 20 # length of substrings
starts <- seq(nchar(df) - 20 + 1)
v1 <- mapply(substr, starts, starts + n - 1, MoreArgs = list(x = df))
names(v1) <- paste0("NAME", seq_along(v1), "\n")
write.table(v1, file = "filename.txt", quote = FALSE, sep = "",
col.names = FALSE)
Randomly replace one or two letters (A-D):
myfun <- function() {
idx <- sample(seq(n), sample(1:2, 1))
rep <- sample(LETTERS[1:4], length(idx), replace = TRUE)
return(list(idx = idx, rep = rep))
}
new <- replicate(length(v1), myfun(), simplify = FALSE)
v2 <- mapply(function(x, y, z) paste(replace(x, y, z), collapse = ""),
strsplit(v1, ""),
lapply(new, "[[", "idx"),
lapply(new, "[[", "rep"))
names(v2) <- paste0(names(v2), ".1")
write.table(v2, file = "filename2.txt", quote = FALSE, sep = "\n",
col.names = FALSE)
I tried breaking this down into multiple simple steps, hopefully you can get learn a few tricks from this:
# Random data
df<-c("ABCBDBDBCBABABDBCBCBDBDBCBDBACDBCCADCDBCDACDDCDACBCDACABACDACABBBCCCBDBDDCACDDACADDDDACCADACBCBDCACD")
n<-10 # Number of cuts
set.seed(1)
# Pick n random numbers between 1 and the length of string-20
nums<-sample(1:(nchar(df)-20),n,replace=TRUE)
# Make your cuts
cuts<-sapply(nums,function(x) substring(df,x,x+20-1))
# Generate some names
nams<-paste0('NAME',1:n)
# Make it into a matrix, transpose, and then recast into a vector to get alternating names and cuts.
names.and.cuts<-c(t(matrix(c(nams,cuts),ncol=2)))
# Drop a file.
write.table(names.and.cuts,'file.txt',quote=FALSE,row.names=FALSE,col.names = FALSE)
# Pick how many changes are going to be made to each cut.
changes<-sample(1:2,n,replace=2)
# Pick that number of positions to change
pos.changes<-lapply(changes,function(x) sample(1:20,x))
# Find the letter at each position.
letter.at.change.pos<-lapply(pos.changes,function(x) substring(df,x,x))
# Make a function that takes any letter, and outputs any other letter from c(A-D)
letter.map<-function(x){
# Make a list of alternate letters.
alternates<-lapply(x,setdiff,x=c('A','B','C','D'))
# Pick one of each
sapply(alternates,sample,size=1)
}
# Find another letter for each
letter.changes<-lapply(letter.at.change.pos,letter.map)
# Make a function to replace character by position
# Inefficient, but who cares.
rep.by.char<-function(str,pos,chars){
for (i in 1:length(pos)) substr(str,pos[i],pos[i])<-chars[i]
str
}
# Change every letter at pos.changes to letter.changes
mod.cuts<-mapply(rep.by.char,cuts,pos.changes,letter.changes,USE.NAMES=FALSE)
# Generate names
nams<-paste0(nams,'.1')
# Use the matrix trick to alternate names.Drop a file.
names.and.mod.cuts<-c(t(matrix(c(nams,mod.cuts),ncol=2)))
write.table(names.and.mod.cuts,'file2.txt',quote=FALSE,row.names=FALSE,col.names = FALSE)
Also, instead of the rep.by.char function, you could just use strsplit and replace like this:
mod.cuts<-mapply(function(x,y,z) paste(replace(x,y,z),collapse=''),
strsplit(cuts,''),pos.changes,letter.changes,USE.NAMES=FALSE)
One way, albeit slowish:
Rgames> foo<-paste(sample(c('a','b','c','d'),20,rep=T),sep='',collapse='')
Rgames> bar<-matrix(unlist(strsplit(foo,'')),ncol=5)
Rgames> bar
[,1] [,2] [,3] [,4] [,5]
[1,] "c" "c" "a" "c" "a"
[2,] "c" "c" "b" "a" "b"
[3,] "b" "b" "a" "c" "d"
[4,] "c" "b" "a" "c" "c"
Now you can select random indices and replace the selected locations with sample(c('a','b','c','d'),1) . For "true" randomness, I wouldn't even force a change - if your newly drawn letter is the same as the original, so be it.
Like this:
ibar<-sample(1:5,4,rep=T) # one random column number for each row
for ( j in 1: 4) bar[j,ibar[j]]<-sample(c('a','b','c','d'),1)
Then, if necessary, recombine each row using paste
For the first part of your question:
df <- c("ABCBDBDBCBABABDBCBCBDBDBCBDBACDBCCADCDBCDACDDCDACBCDACABACDACABBBCCCBDBDDCACDDACADDDDACCADACBCBDCACD")
nstrchars <- 20
count<- nchar(df)-nstrchars
length20substrings <- data.frame(length20substrings=sapply(1:count,function(x)substr(df,x,x+20)))
# to save to a text file. I chose not to include row names or a column name in the .txt file file
write.table(length20substrings,"length20substrings.txt",row.names=F,col.names=F)
For the second part:
# create a function that will randomly pick one or two spots in a string and replace
# those spots with one of the other characters present in the string:
changefxn<- function(x){
x<-as.character(x)
nc<-nchar(as.character(x))
id<-seq(1,nc)
numchanges<-sample(1:2,1)
ids<-sample(id,numchanges)
chars2repl<-strsplit(x,"")[[1]][ids]
charspresent<-unique(unlist(strsplit(x,"")))
splitstr<-unlist(strsplit(x,""))
if (numchanges>1) {
splitstr[id[1]] <- sample(setdiff(charspresent,chars2repl[1]),1)
splitstr[id[2]] <- sample(setdiff(charspresent,chars2repl[2]),1)
}
else {splitstr[id[1]] <- sample(setdiff(charspresent,chars2repl[1]),1)
}
newstr<-paste(splitstr,collapse="")
return(newstr)
}
# try it out
changefxn("asbbad")
changefxn("12lkjaf38gs")
# apply changefxn to all the substrings from part 1
length20substrings<-length20substrings[seq_along(length20substrings[,1]),]
newstrings <- lapply(length20substrings, function(ii)changefxn(ii))
I want to find the pattern from any position in any given string such that the pattern repeats for a threshold number of times at least.
For example for the string "a0cc0vaaaabaaaabaaaabaa00bvw" the pattern should come out to be "aaaab". Another example: for the string "ff00f0f0f0f0f0f0f0f0000" the pattern should be "0f".
In both cases threshold has been taken as 3 i.e. the pattern should be repeated for at least 3 times.
If someone can suggest an optimized method in R for finding a solution to this problem, please do share with me. Currently I am achieving this by using 3 nested loops, and it's taking a lot of time.
Thanks!
Use regular expressions, which are made for this type of stuff. There may be more optimized ways of doing it, but in terms of easy to write code, it's hard to beat. The data:
vec <- c("a0cc0vaaaabaaaabaaaabaa00bvw","ff00f0f0f0f0f0f0f0f0000")
The function that does the matching:
find_rep_path <- function(vec, reps) {
regexp <- paste0(c("(.+)", rep("\\1", reps - 1L)), collapse="")
match <- regmatches(vec, regexpr(regexp, vec, perl=T))
substr(match, 1, nchar(match) / reps)
}
And some tests:
sapply(vec, find_rep_path, reps=3L)
# a0cc0vaaaabaaaabaaaabaa00bvw ff00f0f0f0f0f0f0f0f0000
# "aaaab" "0f0f"
sapply(vec, find_rep_path, reps=5L)
# $a0cc0vaaaabaaaabaaaabaa00bvw
# character(0)
#
# $ff00f0f0f0f0f0f0f0f0000
# [1] "0f"
Note that with threshold as 3, the actual longest pattern for the second string is 0f0f, not 0f (reverts to 0f at threshold 5). In order to do this, I use back references (\\1), and repeat these as many time as necessary to reach threshold. I need to then substr the result because annoyingly base R doesn't have an easy way to get just the captured sub expressions when using perl compatible regular expressions. There is probably a not too hard way to do this, but the substr approach works well in this example.
Also, as per the discussion in #G. Grothendieck's answer, here is the version with the cap on length of pattern, which is just adding the limit argument and the slight modification of the regexp.
find_rep_path <- function(vec, reps, limit) {
regexp <- paste0(c("(.{1,", limit,"})", rep("\\1", reps - 1L)), collapse="")
match <- regmatches(vec, regexpr(regexp, vec, perl=T))
substr(match, 1, nchar(match) / reps)
}
sapply(vec, find_rep_path, reps=3L, limit=3L)
# a0cc0vaaaabaaaabaaaabaa00bvw ff00f0f0f0f0f0f0f0f0000
# "a" "0f"
find.string finds substring of maximum length subject to (1) substring must be repeated consecutively at least th times and (2) substring length must be no longer than len.
reps <- function(s, n) paste(rep(s, n), collapse = "") # repeat s n times
find.string <- function(string, th = 3, len = floor(nchar(string)/th)) {
for(k in len:1) {
pat <- paste0("(.{", k, "})", reps("\\1", th-1))
r <- regexpr(pat, string, perl = TRUE)
if (attr(r, "capture.length") > 0) break
}
if (r > 0) substring(string, r, r + attr(r, "capture.length")-1) else ""
}
and here are some tests. The last test processes the entire text of James Joyce's Ulysses in 1.4 seconds on my laptop:
> find.string("a0cc0vaaaabaaaabaaaabaa00bvw")
[1] "aaaab"
> find.string("ff00f0f0f0f0f0f0f0f0000")
[1] "0f0f"
>
> joyce <- readLines("http://www.gutenberg.org/files/4300/4300-8.txt")
> joycec <- paste(joyce, collapse = " ")
> system.time(result <- find.string2(joycec, len = 25))
user system elapsed
1.36 0.00 1.39
> result
[1] " Hoopsa boyaboy hoopsa!"
ADDED
Although I developed my answer before having seen BrodieG's, as he points out they are very similar to each other. I have added some features of his to the above to get the solution below and tried the tests again. Unfortunately when I added the variation of his code the James Joyce example no longer works although it does work on the other two examples shown. The problem seems to be in adding the len constraint to the code and may represent a fundamental advantage of the code above (i.e. it can handle such a constraint and such constraints may be essential for very long strings).
find.string2 <- function(string, th = 3, len = floor(nchar(string)/th)) {
pat <- paste0(c("(.", "{1,", len, "})", rep("\\1", th-1)), collapse = "")
r <- regexpr(pat, string, perl = TRUE)
ifelse(r > 0, substring(string, r, r + attr(r, "capture.length")-1), "")
}
> find.string2("a0cc0vaaaabaaaabaaaabaa00bvw")
[1] "aaaab"
> find.string2("ff00f0f0f0f0f0f0f0f0000")
[1] "0f0f"
> system.time(result <- find.string2(joycec, len = 25))
user system elapsed
0 0 0
> result
[1] "w"
REVISED The James Joyce test that was supposed to be testing find.string2 was actually using find.string. This is now fixed.
Not optimized (even it is fast) function , but I think it is more R way to do this.
Get all patterns of certains length > threshold : vectorized using mapply and substr
Get the occurrence of these patterns and extract the one with maximum occurrence : vectorized using str_locate_all.
Repeat 1-2 this for all lengths and tkae the one with maximum occurrence.
Here my code. I am creating 2 functions ( steps 1-2) and step 3:
library(stringr)
ss = "ff00f0f0f0f0f0f0f0f0000"
ss <- "a0cc0vaaaabaaaabaaaabaa00bvw"
find_pattern_length <-
function(length=1,ss){
patt = mapply(function(x,y) substr(ss,x,y),
1:(nchar(ss)-length),
(length+1):nchar(ss))
res = str_locate_all(ss,unique(patt))
ll = unlist(lapply(res,length))
list(patt = patt[which.max(ll)],
rep = max(ll))
}
get_pattern_threshold <-
function(ss,threshold =3 ){
res <-
sapply(seq(threshold,nchar(ss)),find_pattern_length,ss=ss)
res[,which.max(res['rep',])]
}
some tests:
get_pattern_threshold('ff00f0f0f0f0f0f0f0f0000',5)
$patt
[1] "0f0f0"
$rep
[1] 6
> get_pattern_threshold('ff00f0f0f0f0f0f0f0f0000',2)
$patt
[1] "f0"
$rep
[1] 18
Since you want at least three repetitions, there is a nice O(n^2) approach.
For each possible pattern length d cut string into parts of length d. In case of d=5 it would be:
a0cc0
vaaaa
baaaa
baaaa
baa00
bvw
Now look at each pairs of subsequent strings A[k] and A[k+1]. If they are equal then there is a pattern of at least two repetitions. Then go further (k+2, k+3) and so on. Finally you also check if suffix of A[k-1] and prefix of A[k+n] fit (where k+n is the first string that doesn't match).
Repeat it for each d starting from some upper bound (at most n/3).
You have n/3 possible lengths, then n/d strings of length d to check for each d. It should give complexity O(n (n/d) d)= O(n^2).
Maybe not optimal but I found this cutting idea quite neat ;)
For a bounded pattern (i.e not huge) it's best I think to just create all possible substrings first and then count them. This is if the sub-patterns can overlap. If not change the step fun in the loop.
pat="a0cc0vaaaabaaaabaaaabaa00bvw"
len=nchar(pat)
thr=3
reps=floor(len/2)
# all poss strings up to half length of pattern
library(stringr)
pat=str_split(pat, "")[[1]][-1]
str.vec=vector()
for(win in 2:reps)
{
str.vec= c(str.vec, rollapply(data=pat,width=win,FUN=paste0, collapse=""))
}
# the max length string repeated more than 3 times
tbl=table(str.vec)
tbl=tbl[tbl>=3]
tbl[which.max(nchar(names(tbl)))]
aaaabaa
3
NB Whilst I'm lazy and append/grow the str.vec here in a loop, for a larger problem I'm pretty sure the actual length of str.vec is predetermined by the length of the pattern if you care to work it out.
Here is my solution, it's not optimized (build vector with patterns <- c() ; pattern <- c(patterns, x) for example) and can be improve but simpler than yours, I think.
I can't understand which pattern exactly should (I just return the max) be returned but you can adjust the code to what you want exactly.
str <- "a0cc0vaaaabaaaabaaaabaa00bvw"
findPatternMax <- function(str){
nb <- nchar(str):1
length.patt <- rev(nb)
patterns <- c()
for (i in 1:length(nb)){
for (j in 1:nb[i]){
patterns <- c(patterns, substr(str, j, j+(length.patt[i]-1)))
}
}
patt.max <- names(which(table(patterns) == max(table(patterns))))
return(patt.max)
}
findPatternMax(str)
> findPatternMax(str)
[1] "a"
EDIT :
Maybe you want the returned pattern have a min length ?
then you can add a nchar.patt parameter for example :
nchar.patt <- 2 #For a pattern of 2 char min
nb <- nb[length.patt >= nchar.patt]
length.patt <- length.patt[length.patt >= nchar.patt]
Long strings in plots aren't always attractive. What's the shortest way of making an acronym in R? E.g., "Hello world" to "HW", and preferably to have unique acronyms.
There's function abbreviate, but it just removes some letters from the phrase, instead of taking first letters of each word.
An easy way would be to use a combination of strsplit, substr, and make.unique.
Here's an example function that can be written:
makeInitials <- function(charVec) {
make.unique(vapply(strsplit(toupper(charVec), " "),
function(x) paste(substr(x, 1, 1), collapse = ""),
vector("character", 1L)))
}
Test it out:
X <- c("Hello World", "Home Work", "holidays with children", "Hello Europe")
makeInitials(X)
# [1] "HW" "HW.1" "HWC" "HE"
That said, I do think that abbreviate should suffice, if you use some of its arguments:
abbreviate(X, minlength=1)
# Hello World Home Work holidays with children Hello Europe
# "HlW" "HmW" "hwc" "HE"
Using regex you can do following. The regex pattern ((?<=\\s).|^.) looks for any letter followed by space or first letter of the string. Then we just paste resulting vectors using collapse argument to get first letter based acronym. And as Ananda suggested, if you want to make unique pass the result through make.unique.
X <- c("Hello World", "Home Work", "holidays with children")
sapply(regmatches(X, gregexpr(pattern = "((?<=\\s).|^.)", text = X, perl = T)), paste, collapse = ".")
## [1] "H.W" "H.W" "h.w.c"
# If you want to make unique
make.unique(sapply(regmatches(X, gregexpr(pattern = "((?<=\\s).|^.)", text = X, perl = T)), paste, collapse = "."))
## [1] "H.W" "H.W.1" "h.w.c"
I would like to convert the a string like be33szfuhm100060 into BESZFUHM0060.
In order to replace the small letters with capital letters I've so far used the gsub function.
test1=gsub("be","BE",test)
Is there a way to tell this function to replace the 3rd and 4th string element? If not, I would really appreciate if you could tell me another way to solve this problem. Maybe there is also a more general solution to change a string element at a certain position into a capital letter whatever the element is?
A couple of observations:
Cnverting a string to uppercase can be done with toupper, e.g.:
> toupper('be33szfuhm100060')
> [1] "BE33SZFUHM100060"
You could use substr to extract a substring by character positions and paste to concatenate strings:
> x <- 'be33szfuhm100060'
> paste(substr(x, 1, 2), substr(x, 5, nchar(x)), sep='')
[1] "beszfuhm100060"
As an alternative, if you are going to be doing this alot:
String <- function(x="") {
x <- as.character(paste(x, collapse=""))
class(x) <- c("String","character")
return(x)
}
"[.String" <- function(x,i,j,...,drop=TRUE) {
unlist(strsplit(x,""))[i]
}
"[<-.String" <- function(x,i,j,...,value) {
tmp <- x[]
tmp[i] <- String(value)
x <- String(tmp)
x
}
print.String <- function(x, ...) cat(x, "\n")
## try it out
> x <- String("be33szfuhm100060")
> x[3:4] <- character(0)
> x
beszfuhm100060
You can use substring to remove the third and fourth elements.
x <- "be33szfuhm100060"
paste(substring(x, 1, 2), substring(x, 5), sep = "")
If you know what portions of the string you want based on their position(s), use substr or substring. As I mentioned in my comment, you can use toupper to coerce characters to uppercase.
paste( toupper(substr(test,1, 2)),
toupper(substr(test,5,10)),
substr(test,12,nchar(test)),sep="")
# [1] "BESZFUHM00060"