On Sep 15, 2011, at 6:00 PM, nikki22 wrote:
Hi, newbie here,
I was wondering if anyone can out, I have checked through the help
archives
but cannot find my answer.
I have three nexus files mostly with the same taxa but some are
different. I
want to concatenate the DNA sequences from these three files into
one large
nexus file but I cannot seem to accomplish it!
This is an example:
file1
taxon1 aaggttcc
taxon2 aagtttcg
taxon3 aaggttcc
file2
taxon2 ctgctg
taxon3 ctggtc
taxon4 ctgctg
file3
taxon1 ggttggtta
taxon2 ggttggttc
taxon4 ggttggttc
dat.mrg <- merge(
merge(file1,file2, by="V1", all=TRUE),
file3,
by="V1", all=TRUE)
> dat.mrg$pseqs <- with(dat.mrg, paste(V2.x , V2.y , V2,
sep=""))
> dat.mrg$pseqs <- gsub("NA", "??????", dat.mrg$pseqs)
> dat.mrg[ , c(1,5)]
V1 pseqs
1 taxon1 aaggttcc??????ggttggtta
2 taxon2 aagtttcgctgctgggttggttc
3 taxon3 aaggttccctggtc??????
4 taxon4 ??????ctgctgggttggttc
this is what i want to end up with (where ? means missing data) in
nexus
format:
taxon1 aaggttcc??????ggttggtta
taxon2 aagtttcgctgctgggttggttc
taxon3 aaggttccctggtc????????
taxon4 ??????????????ggttggttc
Thanks in advance for any help!
David Winsemius, MD
West Hartford, CT
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