R help - Sep 2011 - searching several subsequences in a single string sequence

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?

 

Thanks in advance

 

 

Marcelo Araya-Salas

Ph.D.  Student

Avian Communication and Evolution Lab

Department of Biology

New Mexico State University

Lab: 575-646-4863

 


	[[alternative HTML version deleted]]

Hi Marcelo,

Try this:
x <- "ABCABAABABABCAB"
length(gregexpr(pattern="ABC", x)[[1]])

See ?gregexpr for more details (though I admit that it is not easy to 
understand this help page)

HTH,
Ivan

Le 9/27/2011 18:51, Marcelo Araya a ?crit :
> 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?
>
>
>
> Thanks in advance
>
>
>
>
>
> Marcelo Araya-Salas
>
> Ph.D.  Student
>
> Avian Communication and Evolution Lab
>
> Department of Biology
>
> New Mexico State University
>
> Lab: 575-646-4863
>
>
>
>
> 	[[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.
>
-- 
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Dept. Mammalogy
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calandra at uni-hamburg.de

**********
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php

On Tue, Sep 27, 2011 at 5:51 PM, Marcelo Araya <marceloa27 at 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.