Hi Everyone,
Thanks for all the responses to my question about “find and replace” for my
very large newick strings. This function (thanks to Christie):
gsub("(?<=\\)).*?(?=\\:|\\;)", "", my_newick_string, perl=T) seems to do the
the trick. But thanks to everyone else who responded with other helpful tips.
Cheers,
Karen
On Aug 24, 2015, at 11:35 AM, Karen Gordon <[email protected]> wrote:
> Hi There,
>
> I’m currently wanting to make some changes to some phylogenies in R by
> reading in the newick text as a string, rather than as a phylo object. The
> reason is that the trees are large (~10,000 tips and another set with ~5000
> tips) and I must make changes to a complete set of these tree (i.e. 10,000
> trees). Currently, these trees have node labels, which I’d like to remove.
>
> Essentially what I’d like to do is substitute “)?:” with “):” or simply
> delete "?", where “?" is any and all characters that occur between the
> “close” parenthesis and the colon. So far I found I could use the function
> ’sub’ but I’d like to make the replacements in one fell swoop, without
> knowing what the node labels are in advance. Also the sub function seems to
> only replace the first occurrence of the pattern rather than all matches in a
> string. Any suggestions would be greatly appreciated! Thank you!
>
> best,
> Karen
>
>
>
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