Closed loukesio closed 2 years ago
This issue is very old! I completely missed it, sorry.
How about filtering the matches returned by matchLRPatterns()
to keep only those that have a minimum width? Something like this:
> library(Biostrings)
> dna_string <- DNAString("GTGTGTAAAAANNNNNGTGTNNNNNNNAAAANNNNNNNCCCCCAGAG")
> matches <- matchLRPatterns("AAAA", "CCCCC", 35, dna_string)
> matches
Views on a 47-letter DNAString subject
subject: GTGTGTAAAAANNNNNGTGTNNNNNNNAAAANNNNNNNCCCCCAGAG
views:
start end width
[1] 7 43 37 [AAAAANNNNNGTGTNNNNNNNAAAANNNNNNNCCCCC]
[2] 8 43 36 [AAAANNNNNGTGTNNNNNNNAAAANNNNNNNCCCCC]
[3] 28 43 16 [AAAANNNNNNNCCCCC]
> matches[width(matches) >= 20]
Views on a 47-letter DNAString subject
subject: GTGTGTAAAAANNNNNGTGTNNNNNNNAAAANNNNNNNCCCCCAGAG
views:
start end width
[1] 7 43 37 [AAAAANNNNNGTGTNNNNNNNAAAANNNNNNNCCCCC]
[2] 8 43 36 [AAAANNNNNGTGTNNNNNNNAAAANNNNNNNCCCCC]
This is really a question about basic usage of the package. Note that those questions are better asked on the Bioconductor support site here: https://support.bioconductor.org , where they get a lot more exposure and are more likely to get quick attention.
Best, H.
First of all thank you for maintaining and developing Biostrings and you make our lives better everyday. The following might not be an issue, but mostly its a request/ I am asking for help. Please accept my apologies in advance for taking the advantage. I have a string that looks like this
I want to find a way to extract the sequence between left-pattern=AAAAA and right pattern=CCCCC and allow for mismatches on left and right. I would like to set the minimum distance between left and right pattern to six and the maximum to 30.
Do you have any idea if this is possible? I am aware of the super cool
but in here I can only set the maximum distance and not the minimum?