[Bioc-sig-seq] trimLRPatterns for wild card

[Kunbin Qu]

Harris, thanks so much for the detail explanation. I took what in your first email and it worked perfectly, with the 2nd, it would be better... 

-----Original Message-----
From: Harris A. Jaffee [mailto:hj at jhu.edu] 
Sent: Thursday, September 23, 2010 11:56 AM
To: Kunbin Qu
Cc: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] trimLRPatterns for wild card

Let me try again.  You want Rfixed="subject", only.  Rfixed=FALSE
works in your case by accident since your subject does not contain N.
If it did, the N's would match anything in your pattern, which isn't
what you want.

To clean up another issue, with Rfixed=FALSE, one would expect that
both the pattern and subject would have to be DNA or RNA, and that is
eventually correct.  But, by the time it matters, if your subject is
one of those types, your pattern will have been converted accordingly
for you, automatically.

On Sep 23, 2010, at 2:01 PM, Harris A. Jaffee wrote:
> You need to set 'Rfixed' to either FALSE or "subject":
>
> 	trimLRPatterns(Rpattern=p, subject=a, Rfixed=FALSE)
>
> 	trimLRPatterns(Rpattern=p, subject=a, Rfixed="subject")
>
> See ?matchPattern and ?`lowlevel-matching`.
>
> By the way, your pattern did not have to be a DNAString.  "CCNNT"
> would have been fine.  But the ambiguity machinery with regard to
> the subject requires that it be an RNA- or DNAString.
>
> -Harris
>
> On Sep 23, 2010, at 1:32 PM, Kunbin Qu wrote:
>
>> Hi, all,
>>
>> Does trimLRPatterns function take wild card N? When I tested it,  
>> it does not seem to work. Is there a way to do that? Thanks.
>>
>> -Kunbin
>>
>>
>>> a<-DNAString("AAACCCCTTTCCTTT")
>>> p<-DNAString("CCNNT")
>>> trimLRPatterns(Rpattern=p, subject=a)
>>   15-letter "DNAString" instance
>> seq: AAACCCCTTTCCTTT
>>> p<-DNAString("CCTTT")
>>> trimLRPatterns(Rpattern=p, subject=a)
>>   10-letter "DNAString" instance
>> seq: AAACCCCTTT
>>>
>>
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