[Seqinr-forum] [R] How to parse a string (by a "new" markup) with R ?
Andrej Blejec
Andrej.Blejec at nib.si
Tue Mar 16 23:34:31 CET 2010
A version using regular expressions, lot of regexpr() and substr() functions is attached.
Finally everything is packed into splitSeq() function
Andrej
--
Andrej Blejec
National Institute of Biology
Vecna pot 111 POB 141
SI-1000 Ljubljana
SLOVENIA
e-mail: andrej.blejec at nib.si
URL: http://ablejec.nib.si
tel: + 386 (0)59 232 789
fax: + 386 1 241 29 80
--------------------------
Local Organizer of ICOTS-8
International Conference on Teaching Statistics
http://icots8.org
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Gabor Grothendieck
> Sent: Tuesday, March 16, 2010 3:24 PM
> To: Tal Galili
> Cc: r-help at r-project.org; seqinr-forum at r-forge.wu-wien.ac.at
> Subject: Re: [R] How to parse a string (by a "new" markup) with R ?
>
> We show how to use the gsubfn package to parse this.
>
> The rules are not entirely clear so we will assume the following:
>
> - there is a fixed template for the output which is the same as your
> output but possibly with different character strings filled in. This
> implies, for example, that there are exactly Stem0, Stem1, Stem2 and
> Stem3 and no fewer or more stems.
>
> - the sequence always starts with the open of Stem0, at least one dot
> and the open of Stem1. There are no dots prior to the open of Stem0.
> This seems to be implicit in your sample output since there is no zero
> length string in your sample output corresponding to dots prior to
> Stem0.
>
> - Stem0 closes with the same number of < as there are > to open it
>
> You can modify this yourself to take into account the actual rules
> whatever they are.
>
> We first calculate, k, the number of leading >'s using strapply.
>
> Then we replace the leading k >'s with }'s and the trailing k <'s with
> {'s giving us Str3:
>
>
> "}}}}}}}..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<{{{{{
> {{."
>
> We again use strapply, this time to get the lengths of the runs. Note
> that
> zero length runs are possible so we cannot, for example, use rle for
> this. For
> example there is a zero length run of dots between the last < and the
> first {.
> read.fwf is used to actually parse out the strings using the lengths we
> just
> calculated.
>
> Finally we fill in the template using relist.
>
> # inputs
>
> Seq <-
> "GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGG
> GCA"
> Str <-
> ">>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<
> <<."
> template <-
> list(
> "Stem 0 opening" = "",
> "before Stem 1" = "",
> "Stem 1" = list(opening = "",
> inside = "",
> closing = ""
> ),
> "between Stem 1 and 2" = "",
> "Stem 2" = list(opening = "",
> inside = "",
> closing = ""
> ),
> "between Stem 2 and 3" = "",
> "Stem 3" = list(opening = "",
> inside = "",
> closing = ""
> ),
> "After Stem 3" = "",
> "Stem 0 closing" = ""
> )
>
> # processing
>
> # create string made by repeating string s k times followed by more
> reps <- function(s, k, more = "") {
> paste(paste(rep(s, k), collapse = ""), more, sep = "")
> }
>
> library(gsubfn)
> k <- nchar(strapply(Str, "^>+", c)[[1]])
> Str2 <- sub("^>+", reps("}", k), Str)
> Str3 <- sub(reps("<", k, "([^<]*)$"), reps("{", k, "\\1"), Str2)
>
> pat <-
> "^(}*)([.]*)(>*)([.]*)(<*)([.]*)(>*)([.]*)(<*)([.]*)(>*)([.]*)(<*)([.]*
> )({*)([.]*)$"
> lens <- sapply(strapply(Str3, pat, c)[[1]], nchar)
> tokens <- unlist(read.fwf(textConnection(Seq), lens, as.is = TRUE))
> closeAllConnections()
> tokens[is.na(tokens)] <- ""
> out <- relist(tokens, template)
> out
>
>
> Here is the str of the output for your sample input:
>
> > str(out)
> List of 9
> $ Stem 0 opening : chr "GCCTCGA"
> $ before Stem 1 : chr "TA"
> $ Stem 1 :List of 3
> ..$ opening: chr "GCTC"
> ..$ inside : chr "AGTTGGGA"
> ..$ closing: chr "GAGC"
> $ between Stem 1 and 2: chr "G"
> $ Stem 2 :List of 3
> ..$ opening: chr "TACGA"
> ..$ inside : chr "CTGAAGA"
> ..$ closing: chr "TCGTA"
> $ between Stem 2 and 3: chr "AGGtC"
> $ Stem 3 :List of 3
> ..$ opening: chr "ACCAG"
> ..$ inside : chr "TTCGATC"
> ..$ closing: chr "CTGGT"
> $ After Stem 3 : chr ""
> $ Stem 0 closing : chr "TCGGGGC"
>
>
>
> On Tue, Mar 16, 2010 at 6:10 AM, Tal Galili <tal.galili at gmail.com>
> wrote:
> > Hello all,
> >
> > For some work I am doing on RNA, I want to use R to do string parsing
> that
> > (I think) is like a simplistic HTML parsing.
> >
> >
> > For example, let's say we have the following two variables:
> >
> > Seq <-
> >
> "GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGG
> GCA"
> > Str <-
> >
> ">>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<
> <<."
> >
> > Say that I want to parse "Seq" According to "Str", by using the
> legend here
> >
> > Seq:
> GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGGG
> CA
> > Str:
> >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<
> <.
> >
> > | | | | | | |
> || |
> >
> > +-----+ +--------------+ +---------------+ +---------------
> ++-----+
> >
> > | Stem 1 Stem 2 Stem 3
> |
> >
> > |
> |
> >
> > +-------------------------------------------------------------
> ---+
> >
> > Stem 0
> >
> > Assume that we always have 4 stems (0 to 3), but that the length of
> letters
> > before and after each of them can very.
> >
> > The output should be something like the following list structure:
> >
> >
> > list(
> > "Stem 0 opening" = "GCCTCGA",
> > "before Stem 1" = "TA",
> > "Stem 1" = list(opening = "GCTC",
> > inside = "AGTTGGGA",
> > closing = "GAGC"
> > ),
> > "between Stem 1 and 2" = "G",
> > "Stem 2" = list(opening = "TACGA",
> > inside = "CTGAAGA",
> > closing = "TCGTA"
> > ),
> > "between Stem 2 and 3" = "AGGtC",
> > "Stem 3" = list(opening = "ACCAG",
> > inside = "TTCGATC",
> > closing = "CTGGT"
> > ),
> > "After Stem 3" = "",
> > "Stem 0 closing" = "TCGGGGC"
> > )
> >
> >
> > I don't have any experience with programming a parser, and would like
> > advices as to what strategy to use when programming something like
> this (and
> > any recommended R commands to use).
> >
> >
> > What I was thinking of is to first get rid of the "Stem 0", then go
> through
> > the inner string with a recursive function (let's call it
> "seperate.stem")
> > that each time will split the string into:
> > 1. before stem
> > 2. opening stem
> > 3. inside stem
> > 4. closing stem
> > 5. after stem
> >
> > Where the "after stem" will then be recursively entered into the same
> > function ("seperate.stem")
> >
> > The thing is that I am not sure how to try and do this coding without
> using
> > a loop.
> >
> > Any advices will be most welcomed.
> >
> >
> > ----------------Contact
> > Details:-------------------------------------------------------
> > Contact me: Tal.Galili at gmail.com | 972-52-7275845
> > Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il
> (Hebrew) |
> > www.r-statistics.com (English)
> > ---------------------------------------------------------------------
> -------------------------
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > 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.
> >
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
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