Yes! Thank You, Emmanuel! This works perfectly. In same way I edited also del.rowgapsonly() Sincerely, V.
Dne úterý 2. listopadu 2021 15:12:47 CET, Emmanuel Paradis napsal(a):
> Ha! That's because gaps are coded with dashes in your files; I assumed
> it was X's (as returned by ape::trans). So this line 7 should be:
> foo <- function(x) sum(x == 0x58 | x == 0x2d)
> Or (probably easier to modify):
> foo <- function(x) sum(x == charToRaw("X") | x == charToRaw("-"))
> Cheers,
> Emmanuel
>
> Le 2 Nov 21, à 19:23, Vojtěch Zeisek vo...@trapa.cz a écrit :
> > Thank You, Emmanuel,
> > I thought I must do something with line 7, but I had no idea what.
> > :-) Unfortunately it didn't work. I still get "All sequences of
> > the same length: 249" after running the edited function as 'aln.ng
> > <- del.colgapsonly(x=aln, threshold=0.25, freq.only=FALSE)'... :-(
> > I'm attaching one example (I have almost 1000 of them, so I'd like
> > to avoid to edit all of them manually:-).
> > Sincerely,
> > V.
> >
> > Dne úterý 2. listopadu 2021 12:36:53 CET jste napsal(a):
> >> Hi Vojtěch,
> >> In addition to removing lines 3 and 4, replace line 7:
> >> foo <- function(x) sum(x == 4)
> >> by:
> >> foo <- function(x) sum(x == 0x58)
> >> That sh(c)ould do it.
> >> Best,
> >> Emmanuel
> >>
> >> Le 2 Nov 21, à 17:37, Vojtěch Zeisek vo...@trapa.cz a écrit :
> >> > Hello,
> >> > I try to trim protein alignments in R. I see del.colgapsonly() and
> >> > del.rowgapsonly() from ape can trim only class DNAbin. As DNAbin as
> >> > basically same matrix as AAbin (Isn't it?), I thought it should be
> >> > easy. I commented out lines 3 and 4 in both del.colgapsonly() and
> >> > del.rowgapsonly(), but it didn't lead to success. I haven't found
> >> > any other way how to trim protein alignment in R similar to what
> >> > these two function do. Is there any way?
> >> > Sincerely,
> >> > V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University, Prague, Czech Republic
https://www.natur.cuni.cz/biology/botany/
https://lab-allience.natur.cuni.cz/
https://botany.natur.cuni.cz/brassiploidy/
Institute of Botany, Czech Academy of Sciences
Průhonice, Czech Republic
https://www.ibot.cas.cz/en/
Computing cluster
https://sorbus.ibot.cas.cz/en/start
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