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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