[BioC] report a problem (trimLRPatterns not symmetric?)
Harris A. Jaffee
hj at jhu.edu
Tue Oct 11 20:54:42 CEST 2011
The supposed counter-example (see below) suffers the same inherent
defect as
in your last query: using 'with.*R*indels=T' with an 'Lpattern'.
Fixing that
defect defeats the counter-example, unless I've missed something.
On Oct 11, 2011, at 11:55 AM, wang peter wrote:
> i found a wired problem, but i donot know if it is a bug
>
> triming from left is different from triming from right, please see
> those
> coding
>
> such two sequence have distance of 3
> AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCA
> TCACATCACGATATCGTATGCCGTCTTCTGCTTG
>
> AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
>
> subject<-
> DNAString
> ("AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATA
> TCGTATGCCGTCTTCTGCTTG")
> PCR2rc <-
> DNAString
> ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG")
> trimLRPatterns(Rpattern = PCR2rc, subject = subject,
> max.Rmismatch=0.2,with.Rindels=T)
> or trimLRPatterns(Rpattern = PCR2rc, subject = subject,
> max.Rmismatch=3,with.Rindels=T)
> 25-letter "DNAString" instance
> seq: AAAAAAAAAAAAAAACGACACAAGC
>
> such two sequence are symitric of those above
>
> GATCGGAAGAGCACACGTCTGAACTCCA
> TCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC
> AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
>
> subject<-
> DNAString
> ("GATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAA
> AAAAAAAAACGACACAAGCCC")
> PCR2rc <-
> DNAString
> ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG")
> trimLRPatterns(Lpattern = PCR2rc, subject = subject,
> max.Lmismatch=0.2,with.Rindels=T)
>
> 88-letter "DNAString" instance
> seq:
> ATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAA
> AAAAAACGACACAAGCCC
But,
> trimLRPatterns(Lpattern = PCR2rc, subject = subject,
max.Lmismatch=0.2, with.Lindels=T)
25-letter "DNAString" instance
seq: AAAAAAAAAAAAACGACACAAGCCC
>
> [[alternative HTML version deleted]]
>
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