Dear R-help list, I would like to replace all lower-case letters in a string that are not part of certain fixed expressions. For example, I have the string: "pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))" Where I would like to replace all lower-case letters that do not belong to the functions "pmin" and "pmax" by 1 - toupper(...) to get "pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 - Z1))" Any ideas on how I could achieve that? Many thanks and best wishes, Alrik ******************************** Alrik Thiem Post-Doctoral Researcher Department of Philosophy University of Geneva Rue de Candolle 2 CH-1211 Geneva +41 76 527 80 83 http://www.alrik-thiem.net http://www.compasss.org
If your string will always represent an R expression, you could work with
the expression directly with functions like all.names() and substitute().
f <- function (expr)
{
toReplace <- setdiff(all.names(expr), c("pmin",
"pmax"))
toReplace <- grep(value = TRUE, "[a-z]", toReplace)
names(toReplace) <- toReplace
replacementList <- lapply(toReplace, function(name) call("-",
1, as.name(toupper(name))))
do.call(substitute, list(expr, replacementList))
}
> In <- quote(pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1)))
> Desired <- quote(pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y,
pmax(Z1,
1 - Z1)))> all.equal(Desired, f(In))
[1] TRUE
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Feb 27, 2015 at 2:19 PM, Alrik Thiem <alrik.thiem at gmail.com>
wrote:
> Dear R-help list,
>
> I would like to replace all lower-case letters in a string that are not
> part
> of certain fixed expressions. For example, I have the string:
>
> "pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))"
>
> Where I would like to replace all lower-case letters that do not belong to
> the functions "pmin" and "pmax" by 1 - toupper(...) to
get
>
> "pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 -
Z1))"
>
> Any ideas on how I could achieve that?
>
> Many thanks and best wishes,
>
> Alrik
>
>
> ********************************
> Alrik Thiem
> Post-Doctoral Researcher
>
> Department of Philosophy
> University of Geneva
> Rue de Candolle 2
> CH-1211 Geneva
>
> +41 76 527 80 83
>
> http://www.alrik-thiem.net
> http://www.compasss.org
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
Many thanks. Unfortunately, I cannot work directly on these expressions since
they?re only created from other strings. Would I first have to transform these
strings to unevaluated expressions?
Von: William Dunlap [mailto:wdunlap at tibco.com]
Gesendet: Freitag, 27. Februar 2015 23:39
An: Alrik Thiem
Cc: r-help at r-project.org
Betreff: Re: [R] Substring replacement in string
If your string will always represent an R expression, you could work with
the expression directly with functions like all.names() and substitute().
f <- function (expr)
{
toReplace <- setdiff(all.names(expr), c("pmin",
"pmax"))
toReplace <- grep(value = TRUE, "[a-z]", toReplace)
names(toReplace) <- toReplace
replacementList <- lapply(toReplace, function(name) call("-",
1, as.name(toupper(name))))
do.call(substitute, list(expr, replacementList))
}
> In <- quote(pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1)))
> Desired <- quote(pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y,
pmax(Z1, 1 - Z1)))
> all.equal(Desired, f(In))
[1] TRUE
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Feb 27, 2015 at 2:19 PM, Alrik Thiem <alrik.thiem at gmail.com>
wrote:
Dear R-help list,
I would like to replace all lower-case letters in a string that are not part
of certain fixed expressions. For example, I have the string:
"pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))"
Where I would like to replace all lower-case letters that do not belong to
the functions "pmin" and "pmax" by 1 - toupper(...) to get
"pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 - Z1))"
Any ideas on how I could achieve that?
Many thanks and best wishes,
Alrik
********************************
Alrik Thiem
Post-Doctoral Researcher
Department of Philosophy
University of Geneva
Rue de Candolle 2
CH-1211 Geneva
+41 76 527 80 83
http://www.alrik-thiem.net
http://www.compasss.org
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
On Fri, Feb 27, 2015 at 5:19 PM, Alrik Thiem <alrik.thiem at gmail.com> wrote:> I would like to replace all lower-case letters in a string that are not part > of certain fixed expressions. For example, I have the string: > > "pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))" > > Where I would like to replace all lower-case letters that do not belong to > the functions "pmin" and "pmax" by 1 - toupper(...) to get > > "pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 - Z1))" >Assuming x is the input string: gsub("(\\b[a-oq-z][a-z0-9]+)", "1-\\U\\1", x, perl = TRUE) ## [1] "pmin(pmax(pmin(1-X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1-Z1))" -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com
Dear Gabor, Many thanks. Works like a charm, but I can't get it to work with "pmin(pmax(pmin(a,B),pmin(a,C,d))==Y,pmax(E,e))" i.e., with strings where there're no integers following the components in the pmin/pmax functions. Could this be generalized to handle both cases? Best wishes, Alrik -----Urspr?ngliche Nachricht----- Von: Gabor Grothendieck [mailto:ggrothendieck at gmail.com] Gesendet: Samstag, 28. Februar 2015 13:35 An: Alrik Thiem Cc: r-help at r-project.org Betreff: Re: [R] Substring replacement in string On Fri, Feb 27, 2015 at 5:19 PM, Alrik Thiem <alrik.thiem at gmail.com> wrote:> I would like to replace all lower-case letters in a string that are not part > of certain fixed expressions. For example, I have the string: > > "pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))" > > Where I would like to replace all lower-case letters that do not belong to > the functions "pmin" and "pmax" by 1 - toupper(...) to get > > "pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 - Z1))" >Assuming x is the input string: gsub("(\\b[a-oq-z][a-z0-9]+)", "1-\\U\\1", x, perl = TRUE) ## [1] "pmin(pmax(pmin(1-X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1-Z1))" -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com
Hi Alrik,
With the Biostrings/IRanges infrastructure (Bioconductor packages), you
can do this with:
library(Biostrings)
x0 <- BString("pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1,
z1))")
donttouch_words <- c("pmin", "pmax")
## Extract the substrings to modify (target substrings).
donttouch_regions <- reduce(do.call("c", lapply(donttouch_words,
matchPattern, x0)))
target_regions <- ranges(gaps(donttouch_regions))
target_substrings <- extractAt(x0, target_regions)
## Modify them.
old <- paste0(letters, collapse="")
new <- paste0(LETTERS, collapse="")
target_substrings <- chartr(old, new, target_substrings)
## Replace in original string.
x1 <- replaceAt(x0, target_regions, target_substrings)
Then:
> x1
57-letter "BString" instance
seq: pmin(pmax(pmin(X1, X2), pmin(X3, X4)) == Y, pmax(Z1, Z1))
> as.character(x1)
[1] "pmin(pmax(pmin(X1, X2), pmin(X3, X4)) == Y, pmax(Z1, Z1))"
Hope this helps,
H.
On 02/27/2015 02:19 PM, Alrik Thiem wrote:> Dear R-help list,
>
> I would like to replace all lower-case letters in a string that are not
part
> of certain fixed expressions. For example, I have the string:
>
> "pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))"
>
> Where I would like to replace all lower-case letters that do not belong to
> the functions "pmin" and "pmax" by 1 - toupper(...) to
get
>
> "pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 -
Z1))"
>
> Any ideas on how I could achieve that?
>
> Many thanks and best wishes,
>
> Alrik
>
>
> ********************************
> Alrik Thiem
> Post-Doctoral Researcher
>
> Department of Philosophy
> University of Geneva
> Rue de Candolle 2
> CH-1211 Geneva
>
> +41 76 527 80 83
>
> http://www.alrik-thiem.net
> http://www.compasss.org
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
Dear Herv?,
Many thanks for your suggestion. Gabor Grothendieck proposed a simple
one-liner that works perfectly for my purposes:
gsub("(\\b[a-oq-z][a-z0-9]*)", "1-\\U\\1", x, perl = TRUE)
where x is the respective string.
Best wishes,
Alrik
-----Urspr?ngliche Nachricht-----
Von: Herv? Pag?s [mailto:hpages at fredhutch.org]
Gesendet: Samstag, 28. Februar 2015 23:29
An: Alrik Thiem; r-help at r-project.org
Betreff: Re: [R] Substring replacement in string
Hi Alrik,
With the Biostrings/IRanges infrastructure (Bioconductor packages), you
can do this with:
library(Biostrings)
x0 <- BString("pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1,
z1))")
donttouch_words <- c("pmin", "pmax")
## Extract the substrings to modify (target substrings).
donttouch_regions <- reduce(do.call("c", lapply(donttouch_words,
matchPattern, x0)))
target_regions <- ranges(gaps(donttouch_regions))
target_substrings <- extractAt(x0, target_regions)
## Modify them.
old <- paste0(letters, collapse="")
new <- paste0(LETTERS, collapse="")
target_substrings <- chartr(old, new, target_substrings)
## Replace in original string.
x1 <- replaceAt(x0, target_regions, target_substrings)
Then:
> x1
57-letter "BString" instance
seq: pmin(pmax(pmin(X1, X2), pmin(X3, X4)) == Y, pmax(Z1, Z1))
> as.character(x1)
[1] "pmin(pmax(pmin(X1, X2), pmin(X3, X4)) == Y, pmax(Z1, Z1))"
Hope this helps,
H.
On 02/27/2015 02:19 PM, Alrik Thiem wrote:> Dear R-help list,
>
> I would like to replace all lower-case letters in a string that are not
part> of certain fixed expressions. For example, I have the string:
>
> "pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))"
>
> Where I would like to replace all lower-case letters that do not belong to
> the functions "pmin" and "pmax" by 1 - toupper(...) to
get
>
> "pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 -
Z1))"
>
> Any ideas on how I could achieve that?
>
> Many thanks and best wishes,
>
> Alrik
>
>
> ********************************
> Alrik Thiem
> Post-Doctoral Researcher
>
> Department of Philosophy
> University of Geneva
> Rue de Candolle 2
> CH-1211 Geneva
>
> +41 76 527 80 83
>
> http://www.alrik-thiem.net
> http://www.compasss.org
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319