Re: [R-sig-phylo] Trimming protein alignment
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 signature.asc Description: This is a digitally signed message part. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Trimming protein alignment
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/ > > 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 > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Trimming protein alignment
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/ 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 >Musa MFSSFSSSGDPSLHHPEFCSATSPQGLFPDANSAFPSSSPPCTSFSSESYLHTHSLPFHHHYIPDSLNQPLYSSSPCDYLDFNAGPVRRVLSTGNLQGGNGLHENSSQEGGVAGKVGRYSAEERKERIERYRSKRNQRNFHKKITYECRKTLADSRPRVRGRFARNGETETEAAVEMETGTDTGAAAVNCFDNYEQNQLGGNGSDCWRQLQAALAMDDEDEYSYDEEFLASFSDFYSMNTL >C1 HPPYCDYLDFKAGPVRR >C2 CDYLDFHAAPVR- >C3 -YFDWSIGAHSRPLHHHIA--ELIYPTYSSSPCDYLDFNAEPVRR >C4 -YFDGSISAHSRPLHHHVA--ELIYPTYSSSPCDYLDFNAEPVRR >C5 CDYLDFHAAPVR- >C6 -YFDGSISAHSRPLHHHVA--ELIYPTYSSSPCDYLDFNAEPVRR >C7 CDYLDFHAAPVR- signature.asc Description: This is a digitally signed message part. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Trimming protein alignment
Hello, thank You, but it seems that trimEnds() requires DNAbin. I checked also other functions from ips, and it seems to be the same... Sincerely, V. Dne úterý 2. listopadu 2021 12:13:06 CET jste napsal(a): > Dear Vojtech, > Did you check this https://rdrr.io/cran/ips/man/trimEnds.html > Franz > > > On 2. Nov 2021, at 11:38, Vojtěch Zeisek wrote: > > 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/ 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 signature.asc Description: This is a digitally signed message part. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Trimming protein alignment
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/ > > 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 > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/