matchPattern does not support your non-integral setting
max.mismatch=0.2.
The help page is very clear about that with the phrase "number of ...":
max.mismatch, min.mismatch: The maximum and minimum number of
mismatching letters allowed
Your 0.2 is converted to 0L by as.integer(max.mismatch), as here:
> Biostrings:::normargMaxMismatch(0.2)
[1] 0
I think the following call gives what you want:
> matchPattern(pattern1, subject1, max.mismatch=1, with.indels=TRUE)
Views on a 81-letter BString subject
subject:
ATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCC...TATGCCGTCTTCTGCTTGAAAAAAAAAAAATATT
views:
start end width
[1] 1 65 65
[ATCGAGATCGGAAGAGCGGTTCAGCAGG...CCGATCTCGTATGCCGTCTTCTGCTTG]
However, the trimLRPatterns call you wrote is suspicious because you
don't
mention any 'subject' (only *subject1*):
trimLRPatterns(Lpattern = pattern1, subject = subject,
max.Lmismatch=0,with.Lindels=TRUE)
But, if we use subject1 instead there, we get
> trimLRPatterns(Lpattern = pattern1, subject = subject1,
max.Lmismatch=0,
with.Lindels=TRUE)
[1] "AAAAAAAAAAAATATT"
And this happens because of:
> pattern_suffix = substr(pattern1, start=2, stop=nchar(pattern1))
> neditAt(at=1, pattern_suffix, subject1, with.indels=TRUE)
[1] 0
On Sep 27, 2011, at 3:23 PM, wang peter wrote:
hello every one,
i have such coding
subject1 =
"ATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAA
AAAAAAAATATT"
pattern1 =
"AATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG"
matchPattern(pattern1, subject1, max.mismatch=0.2, min.mismatch=0,
with.indels=TRUE)
Views on a 81-letter BString subject
subject:
ATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAA
AAAAAAATATT
views: NONE
trimLRPatterns(Lpattern = pattern1, subject = subject,
max.Lmismatch=0,with.Lindels=TRUE)
[1] "AAAAAAAAAAAATATT"
i already allow the indels,but why matchPattern cannot find the
pattern in
subject
what does with.indels mean?
i am confused
thx
shan gao
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