thanks for the clarification.
## Fails
>
trimLRPatterns(Rpattern=reverse(pattern),subject=reverse(subjectSet),max.Rmismatch=rep(1,nchar(pattern)),
with.Rindels=TRUE)
Error in .matchPatternAt(pattern, subject, ending.at, 1L, max.mismatch, :
_nedit_for_Proffset() is not ready yet, sorry!
rPattern <- reverse(pattern)
rSubjectSet <- reverse(DNAStringSet(subjectSet, 1, min(width(subjectSet))))
print(rSubjectSet)
A DNAStringSet instance of length 3
width seq names
[1] 42 GGGGGGGGGGGGGGGGGGGGTGAGACGCAACTATGGTGACGA Primer0+poly(T)
[2] 42 GGGGGGGGGGGGGGGGGGGTGAGACGCAACTATGGTGACGAA Primer1+poly(T)
[3] 42 GGGGGGGGGGGGGGGGGGTGAGACGCAACTATGGTGACGAAA Primer2+poly(T)
## fixed width example to reverse
trimLRPatterns(Rpattern=rPattern, subject=rSubjectSet,
max.Rmismatch=rep(1,nchar(pattern)), with.Rindels=TRUE)
A DNAStringSet instance of length 3
width seq names
[1] 20 GGGGGGGGGGGGGGGGGGGG Primer0+poly(T)
[2] 19 GGGGGGGGGGGGGGGGGGG Primer1+poly(T)
[3] 19 GGGGGGGGGGGGGGGGGGT Primer2+poly(T)
Marcus
On Thu, Jan 28, 2010 at 11:13 AM, Harris A. Jaffee <[email protected]> wrote:
> Actually, your 'subjectSet' had non-constant width. This caused
> trimLRPatterns (any version
> from Bioconductor!) for an Rpattern to reverse everything and work on the
> left. This results
> in a call to _nedit_for_Proffset (for the indels situation), which isn't
> written yet. You'll
> have the same failure on ANY call for an Lpattern, with with.Lindels
> TRUE, regardless of the
> subject widths. If your subjectSet had had constant width, the call below
> for the Rpattern
> would have worked fine.
>
> The version of mine that I alluded to avoids Proffset, but it has slightly
> different results:
>
> ... demands that matches-with-indels start at the beginning
> of the subject, for Lpattern, and end at the end of the subject, for
> Rpattern.
>
> I think this follows the "spec" (and that the current version does not),
> but others might not
> agree or like my results. I'll submit a patch, along with a laundry list
> of cases.
>
> On Jan 27, 2010, at 4:27 PM, Marcus Davy wrote:
>
> the arg 'with.Rindels' functionality in trimLRPatterns is not in the
> current stable release of Bioconductor 2.5, you need to install the
> development version
>
> >
> trimLRPatterns(Rpattern=reverse(pattern),subject=reverse(subjectSet),max.Rmismatch=rep(1,nchar(pattern)),
> with.Rindels=TRUE)
> Error in .matchPatternAt(pattern, subject, *ending.at* <http://ending.at/>,
> 1L, max.mismatch, :
> _nedit_for_Proffset() is not ready yet, sorry!
> >
>
>
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