Is there an easy way to replace a sub-list of strings in a character vector with another list of strings? something like
gsub(c("a","b"),c("z","y"),a)
or
replace(a,c("a","b"),c("z","y"))
neither of which unfortunately work?
If you are just replacing single characters, then chartr might just be what you are looking for :
> chartr( "ab", "zy", "abababa")
[1] "zyzyzyz"
This question might also be of interest.
A simple loop using gsub would suffice and will probably perform just fine in most cases:
a <- c("x","y")
b <- c("a","b")
vec <- "xy12"
mgsub <- function(pattern,replacement,x,...){
for (i in seq_along(pattern)){
x <- gsub(pattern = pattern[i],replacement = replacement[i],x,...)
}
x
}
> mgsub(a,b,vec)
[1] "ab12"
I could've sworn there was a recursive apply in R, and there is, but it does something very different.
Anyhow, here's one:
#' Iteratively (recursively) apply a function to its own output
#' #param X a vector of first arguments to be passed in
#' #param FUN a function taking a changing (x) and an initial argument (init)
#' #param init an argument to be "worked on" by FUN with parameters x[1], x[2], etc.
#' #return the final value, of the same type as init
#' #example
#' vec <- "xy12"
#' replacementPairs <- list( c("x","a"), c("y","b") )
#' iapply( replacementPairs , FUN=function(repvec,x) {
#' gsub(repvec[1],repvec[2],x)
#' }, init=vec )
iapply <- function(X, FUN, init, ...) {
res <- init
for(x in X) {
res <- FUN(x, res, ...)
}
res
}
The example returns "ab12".
Related
(This code doesn't make much sense, but I need this logic to work in my other complicated function):
import Data.List
elemIndex1 xss#(x:xs) =
if (x == ' ')
then (elemIndex x xss)
else (elemIndex1 xs)
So I want this function to give this:
elemIndex1 "qwe asd zxc"
Just 3
Instead it gives this:
elemIndex1 "qwe asd zxc"
Just 0
As I understand, at the else clause xss actually becomes xs.
So my question is: is there a possibility to bind the variable (x:xs) to a constant and to use this constant at any iteration?
It seems like you are expecting xss#(x:xs) to be the following:
xss: the original string given to elemIndex1
x: the first character of an arbitrary call
xs: the rest of the characters of an arbitrary call
e.g. for your example when x first matches a space
xss = "qwe asd zxc"
x = ' '
xs = "asd zxe"
This is not how the pattern match works. xss is actually equal to x:xs, so in that example it would be " asd zxc".
If you want to keep around the first call to a function, you can use a helper function called inside of the scope of the original function.
weirdElemIndex str = weirdElemIndex' str
where
weirdElemIndex' "" = Nothing
weirdElemIndex' (x:xs) =
if x == ' '
then elemIndex ' ' str
else weirdElemIndex' xs
Note that the str I reference in the body of the helper function will be a constant in its invocation.
For what it’s worth, your contrived example seems to be equivalent to elemIndex ' ' since it deals with the case where there is no space in the string by returning Nothing.
I am expecting the code below to print chr7.
import strutils
var splitLine = "chr7 127471196 127472363 Pos1 0 +".split()
var chrom, startPos, endPos = splitLine[0..2]
echo chrom
Instead it prints #[chr7, 127471196, 127472363].
Is there a way to unpack multiple values from sequences at the same time?
And what would the tersest way to do the above be if the elements weren't contiguous? For example:
var chrom, startPos, strand = splitLine[0..1, 5]
Gives the error:
read_bed.nim(8, 40) Error: type mismatch: got (seq[string], Slice[system.int], int literal(5))
but expected one of:
system.[](a: array[Idx, T], x: Slice[system.int])
system.[](s: string, x: Slice[system.int])
system.[](a: array[Idx, T], x: Slice[[].Idx])
system.[](s: seq[T], x: Slice[system.int])
var chrom, startPos, strand = splitLine[0..1, 5]
^
This can be accomplished using macros.
import macros
macro `..=`*(lhs: untyped, rhs: tuple|seq|array): auto =
# Check that the lhs is a tuple of identifiers.
expectKind(lhs, nnkPar)
for i in 0..len(lhs)-1:
expectKind(lhs[i], nnkIdent)
# Result is a statement list starting with an
# assignment to a tmp variable of rhs.
let t = genSym()
result = newStmtList(quote do:
let `t` = `rhs`)
# assign each component to the corresponding
# variable.
for i in 0..len(lhs)-1:
let v = lhs[i]
# skip assignments to _.
if $v.toStrLit != "_":
result.add(quote do:
`v` = `t`[`i`])
macro headAux(count: int, rhs: seq|array|tuple): auto =
let t = genSym()
result = quote do:
let `t` = `rhs`
()
for i in 0..count.intVal-1:
result[1].add(quote do:
`t`[`i`])
template head*(count: static[int], rhs: untyped): auto =
# We need to redirect this through a template because
# of a bug in the current Nim compiler when using
# static[int] with macros.
headAux(count, rhs)
var x, y: int
(x, y) ..= (1, 2)
echo x, y
(x, _) ..= (3, 4)
echo x, y
(x, y) ..= #[4, 5, 6]
echo x, y
let z = head(2, #[4, 5, 6])
echo z
(x, y) ..= head(2, #[7, 8, 9])
echo x, y
The ..= macro unpacks tuple or sequence assignments. You can accomplish the same with var (x, y) = (1, 2), for example, but ..= works for seqs and arrays, too, and allows you to reuse variables.
The head template/macro extracts the first count elements from a tuple, array, or seqs and returns them as a tuple (which can then be used like any other tuple, e.g. for destructuring with let or var).
For anyone that's looking for a quick solution, here's a nimble package I wrote called unpack.
You can do sequence and object destructuring/unpacking with syntax like this:
someSeqOrTupleOrArray.lunpack(a, b, c)
[a2, b2, c2] <- someSeqOrTupleOrArray
{name, job} <- tim
tom.lunpack(job, otherName = name)
{job, name: yetAnotherName} <- john
Currently pattern matching in Nim only works with tuples. This also makes sense, because pattern matching requires a statically known arity. For instance, what should happen in your example, if the seq does not have a length of three? Note that in your example the length of the sequence can only be determined at runtime, so the compiler does not know if it is actually possible to extract three variables.
Therefore I think the solution which was linked by #def- was going in the right direction. This example uses arrays, which do have a statically known size. In this case the compiler knows the tuple arity, i.e., the extraction is well defined.
If you want an alternative (maybe convenient but unsafe) approach you could do something like this:
import macros
macro extract(args: varargs[untyped]): typed =
## assumes that the first expression is an expression
## which can take a bracket expression. Let's call it
## `arr`. The generated AST will then correspond to:
##
## let <second_arg> = arr[0]
## let <third_arg> = arr[1]
## ...
result = newStmtList()
# the first vararg is the "array"
let arr = args[0]
var i = 0
# all other varargs are now used as "injected" let bindings
for arg in args.children:
if i > 0:
var rhs = newNimNode(nnkBracketExpr)
rhs.add(arr)
rhs.add(newIntLitNode(i-1))
let assign = newLetStmt(arg, rhs) # could be replaced by newVarStmt
result.add(assign)
i += 1
#echo result.treerepr
let s = #["X", "Y", "Z"]
s.extract(a, b, c)
# this essentially produces:
# let a = s[0]
# let b = s[1]
# let c = s[2]
# check if it works:
echo a, b, c
I do not have included a check for the seq length yet, so you would simply get out-of-bounds error if the seq does not have the required length. Another warning: If the first expression is not a literal, the expression would be evaluated/calculated several times.
Note that the _ literal is allowed in let bindings as a placeholder, which means that you could do things like this:
s.extract(a, b, _, _, _, x)
This would address your splitLine[0..1, 5] example, which btw is simply not a valid indexing syntax.
yet another option is package definesugar:
import strutils, definesugar
# need to use splitWhitespace instead of split to prevent empty string elements in sequence
var splitLine = "chr7 127471196 127472363 Pos1 0 +".splitWhitespace()
echo splitLine
block:
(chrom, startPos, endPos) := splitLine[0..2]
echo chrom # chr7
echo startPos # 127471196
echo endPos # 127472363
block:
(chrom, startPos, strand) := splitLine[0..1] & splitLine[5] # splitLine[0..1, 5] not supported
echo chrom
echo startPos
echo strand # +
# alternative syntax
block:
(chrom, startPos, *_, strand) := splitLine
echo chrom
echo startPos
echo strand
see https://forum.nim-lang.org/t/7072 for recent discussion
I am working on some of the exercism.io exercises. The current one I am working on is for Scala DNA exercise. Here is my code and the errors that I am receiving:
For reference, DNA is instantiated with a strand String. This DNA can call count (which counts the strand for the single nucleotide passed) and nucletideCounts which counts all of the respective occurrences of each nucleotide in the strand and returns a Map[Char,Int].
class DNA(strand:String) {
def count(nucleotide:Char): Int = {
strand.count(_ == nucleotide)
}
def nucleotideCounts = (
for {
n <- strand
c <- count(n)
} yield (n, c)
).toMap
}
The errors I am receiving are:
Error:(10, 17) value map is not a member of Int
c <- count(n)
^
Error:(12, 5) Cannot prove that Char <:< (T, U). ).toMap
^
Error:(12, 5) not enough arguments for method toMap: (implicit ev:
<:<[Char,(T, U)])scala.collection.immutable.Map[T,U]. Unspecified
value parameter ev. ).toMap
^
I am quite new to Scala, so any enlightenment on why these errors are occurring and suggestions to fixing them would be greatly appreciated.
for comprehensions work over Traversable's that have flatMap and map methods defined, as the error message is pointing out.
In your case count returns with a simple integer so no need to "iterate" over it, just simply add it to your result set.
for {
n <- strand
} yield (n, count(n))
On a side note this solution is not too optimal as in the case of a strand AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA count is going to be called many times. I would recommend calling toSet so you get the distinct Chars only:
for {
n <- strand.toSet
} yield (n, count(n))
In line with Akos's approach, consider a parallel traversal of a given strand (String),
strand.distinct.par.map( n => n -> count(n) )
Here we use distinct to gather unique items and construct each Map association in map.
A pipeline solution would look like:
def nucleotideCounts() = strand.groupBy(identity).mapValues(_.length)
Another approach is
Map() ++ {for (n <- strand; c = count(n)) yield n->c}
Not sure why it's different than {...}.toMap() but it gets the job done!
Another way to go is
Map() ++ {for (n <- strand; c <- Seq(count(n))) yield n->c}
This works
x <- "0.466:1.187:2.216:1.196"
y <- as.numeric(unlist(strsplit(x, ":")))
Values of blat$LRwAvg all look like X above but this doesn't work
for (i in 1:50){
y <- as.numeric(unlist(strsplit(blat$LRwAvg[i], "\\:")))
blat$meanLRwAvg[i]=mean(y)
}
Because of:
Error in strsplit(blat$LRwAvg[i], "\:") : non-character argument
It doesn't matter if I have one, two or null backslashes.
What's my problem? (Not generally, I mean in this special task, technically)
As agstudy implied blat$LRwAvg <- as.character(blat$LRwAvg) before loop fixed it
blat$meanLRwAvg <- blat$gtFrqAvg #or some other variable in data frame with equal length
blat$LRwAvg <- as.character(blat$LRwAvg)
for (i in 1:50){
y <- as.numeric(unlist(strsplit(blat$LRwAvg[i], "\\:")))
blat$meanLRwAvg[i]=mean(y)
}
I would like to insert an extra character (or a new string) at a specific location in a string. For example, I want to insert d at the fourth location in abcefg to get abcdefg.
Now I am using:
old <- "abcefg"
n <- 4
paste(substr(old, 1, n-1), "d", substr(old, n, nchar(old)), sep = "")
I could write a one-line simple function for this task, but I am just curious if there is an existing function for that.
You can do this with regular expressions and gsub.
gsub('^([a-z]{3})([a-z]+)$', '\\1d\\2', old)
# [1] "abcdefg"
If you want to do this dynamically, you can create the expressions using paste:
letter <- 'd'
lhs <- paste0('^([a-z]{', n-1, '})([a-z]+)$')
rhs <- paste0('\\1', letter, '\\2')
gsub(lhs, rhs, old)
# [1] "abcdefg"
as per DWin's comment,you may want this to be more general.
gsub('^(.{3})(.*)$', '\\1d\\2', old)
This way any three characters will match rather than only lower case. DWin also suggests using sub instead of gsub. This way you don't have to worry about the ^ as much since sub will only match the first instance. But I like to be explicit in regular expressions and only move to more general ones as I understand them and find a need for more generality.
as Greg Snow noted, you can use another form of regular expression that looks behind matches:
sub( '(?<=.{3})', 'd', old, perl=TRUE )
and could also build my dynamic gsub above using sprintf rather than paste0:
lhs <- sprintf('^([a-z]{%d})([a-z]+)$', n-1)
or for his sub regular expression:
lhs <- sprintf('(?<=.{%d})',n-1)
stringi package for the rescue once again! The most simple and elegant solution among presented ones.
stri_sub function allows you to extract parts of the string and substitute parts of it like this:
x <- "abcde"
stri_sub(x, 1, 3) # from first to third character
# [1] "abc"
stri_sub(x, 1, 3) <- 1 # substitute from first to third character
x
# [1] "1de"
But if you do this:
x <- "abcde"
stri_sub(x, 3, 2) # from 3 to 2 so... zero ?
# [1] ""
stri_sub(x, 3, 2) <- 1 # substitute from 3 to 2 ... hmm
x
# [1] "ab1cde"
then no characters are removed but new one are inserted. Isn't that cool? :)
#Justin's answer is the way I'd actually approach this because of its flexibility, but this could also be a fun approach.
You can treat the string as "fixed width format" and specify where you want to insert your character:
paste(read.fwf(textConnection(old),
c(4, nchar(old)), as.is = TRUE),
collapse = "d")
Particularly nice is the output when using sapply, since you get to see the original string as the "name".
newold <- c("some", "random", "words", "strung", "together")
sapply(newold, function(x) paste(read.fwf(textConnection(x),
c(4, nchar(x)), as.is = TRUE),
collapse = "-WEE-"))
# some random words strung together
# "some-WEE-NA" "rand-WEE-om" "word-WEE-s" "stru-WEE-ng" "toge-WEE-ther"
Your original way of doing this (i.e. splitting the string at an index and pasting in the inserted text) could be made into a generic function like so:
split_str_by_index <- function(target, index) {
index <- sort(index)
substr(rep(target, length(index) + 1),
start = c(1, index),
stop = c(index -1, nchar(target)))
}
#Taken from https://stat.ethz.ch/pipermail/r-help/2006-March/101023.html
interleave <- function(v1,v2)
{
ord1 <- 2*(1:length(v1))-1
ord2 <- 2*(1:length(v2))
c(v1,v2)[order(c(ord1,ord2))]
}
insert_str <- function(target, insert, index) {
insert <- insert[order(index)]
index <- sort(index)
paste(interleave(split_str_by_index(target, index), insert), collapse="")
}
Example usage:
> insert_str("1234567890", c("a", "b", "c"), c(5, 9, 3))
[1] "12c34a5678b90"
This allows you to insert a vector of characters at the locations given by a vector of indexes. The split_str_by_index and interleave functions are also useful on their own.
Edit:
I revised the code to allow for indexes in any order. Before, indexes needed to be in ascending order.
I've made a custom function called substr1 to deal with extracting, replacing and inserting chars in a string. Run these codes at the start of every session. Feel free to try it out and let me know if it needs to be improved.
# extraction
substr1 <- function(x,y) {
z <- sapply(strsplit(as.character(x),''),function(w) paste(na.omit(w[y]),collapse=''))
dim(z) <- dim(x)
return(z) }
# substitution + insertion
`substr1<-` <- function(x,y,value) {
names(y) <- c(value,rep('',length(y)-length(value)))
z <- sapply(strsplit(as.character(x),''),function(w) {
v <- seq(w)
names(v) <- w
paste(names(sort(c(y,v[setdiff(v,y)]))),collapse='') })
dim(z) <- dim(x)
return(z) }
# demonstration
abc <- 'abc'
substr1(abc,1)
# "a"
substr1(abc,c(1,3))
# "ac"
substr1(abc,-1)
# "bc"
substr1(abc,1) <- 'A'
# "Abc"
substr1(abc,1.5) <- 'A'
# "aAbc"
substr1(abc,c(0.5,2,3)) <- c('A','B')
# "AaB"
It took me some time to understand the regular expression, afterwards I found my way with the numbers I had
The end result was
old <- "89580000"
gsub('^([0-9]{5})([0-9]+)$', '\\1-\\2', old)
similar to yours!
First make sure to load tidyverse package, and then use both paste0 and gsub.
Here is the exact code:
paste0(substr(old, 1,3), "d", substr(old,4,6))
In base you can use regmatches to insert a character at a specific location in a string.
old <- "abcefg"
n <- 4
regmatches(old, `attr<-`(n, "match.length", 0)) <- "d"
old
#[1] "abcdefg"
This could also be used with a regex to find the location to insert.
s <- "abcefg"
regmatches(s, regexpr("(?<=c)", s, perl=TRUE)) <- "d"
s
#[1] "abcdefg"
And works also for multiple matches with individual repacements at different matches.
s <- "abcefg abcefg"
regmatches(s, gregexpr("(?<=c)", s, perl=TRUE)) <- list(1:2)
s
#[1] "abc1efg abc2efg"