Barry Rowlingson wrote on 09/27/2011 12:06:21 PM:
>
> On Tue, Sep 27, 2011 at 5:51 PM, Marcelo Araya <marcelo...@gmail.com>
wrote:
> > Hi all
> >
> >
> >
> > I am analyzing bird song element sequences. I would like to know how
can I
> > get how many times a given subsequence is found in single string
sequence.
> >
> >
> >
> >
> >
> > For example:
> >
> >
> >
> > If I have this single sequence:
> >
> >
> >
> > ABCABAABABABCAB
> >
> >
> >
> > I am looking for the subsequence "ABC". Want I need to get here is
that the
> > subsequence is found twice.
> >
> >
> >
> > Any idea how can I do this?
> >
>
> gregexpr will return the position and length of multiple matches. And
> you can feed it a vector. So:
>
>
> > songs=c("ABCABAABABABCAB","ABACAB","ABABCABCBC")
> > gregexpr(m,songs)
> [[1]]
> [1] 1 11
> attr(,"match.length")
> [1] 3 3
>
> [[2]]
> [1] -1
> attr(,"match.length")
> [1] -1
>
> [[3]]
> [1] 3 6
> attr(,"match.length")
> [1] 3 3
>
> - in the first item, it was found at posn 1 and 11
> - in the second it wasnt found at all
> - in the third, it was found at posn 3 and 6
>
> so just do some apply-ing to the returned list and get the length of
> each element. Job done!
>
> Barry
>
> PS bonus points for spotting the hidden prog-rock song title.
For example,
songs <- c("ABCABAABABABCAB", "ABACAB", "ABABCABCBC")
counts <- gregexpr("ABC", songs)
sapply(counts, length)
Jean
P.S. 1981 Genesis album!
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