Hello, i'm new in this list, and new in genetics field too.
I'm reading a book "Analysis of Phylogenetics and Evolution with R" and in
the book i saw about the function query() of the package seqinr to search
databases about specific sequences of our interest.
#A got a list of some frog species:
lista.spp<-c("Rhinella rubescens", "Rhinella fernandezae", "Elosia
rustica",
"Crossodactylus gaudichaudii", "Leptodactylus pustulatus", "Leptodactylus
syphax",
"Dendropsophus cachimbo", "Leptodactylus marmoratus", "Physalaemus
soaresi",
"Hylodes nasus", "Scinax fuscomarginatus", "Leptodactylus petersii",
"Chiasmocleis capixaba", "Ceratophrys aurita", "Pleurodema diplolister",
"Cystignatus gigas", "Scinax trilineatus", "Elosis nasus", "Dryadophis
bifossatus"
)
#And stared looking for 16s RIBOSOMAL RNA.
#My problem is that for some species it worked great.
#For example:
> library(seqinr)
> s <- choosebank("genbank")
> query("SP","SP=Rhinella rubescens AND K=16S RIBOSOMAL RNA",s$socket)
> SP$nelem
[1] 1
> getName(SP)
[1] "GU907196.RR1"
#1 sequence and the name to get the sequence later
> query("SP","SP=Leptodactylus syphax AND K=16S RIBOSOMAL RNA",s$socket)
> print(SP$nelem)
[1] 2
> print(getName(SP))
[1] "JF789923" "JF789924"
#2 sequences and names to get them later.
#The problems is that for some species like
> query("SP","SP=Leptodactylus marmoratus AND K=16S RIBOSOMAL RNA",s$socket)
R stops, i thought it would return too many information, but even using the
argument virtual=T it stops the same way, and i have to turn R off.
I looked in the genbank site and this species should return no sequence but
i don't know what is wrong.
Also, in my understanding, "Leptodactylus syphax" should return 2
sequences, looking in genbank site, but it also stops.
But from the 19 species, only some stops, the others work, i cant figure
out what is happening.
I use windows 7 OS, a residential internet, R 2.15.0 and Tinn-R as a R-gui
Also, in the university the port query() function use is blocked, only
ports like 80 are open in the firewall, are there other functions like this
in R?
In the task view, biocondutor project was cited but i still searching there.
Could someone enlighten me?
Best Wishes
Augusto Ribas
--
Grato
Augusto C. A. Ribas
Site Pessoal: http://augustoribas.heliohost.org
Lattes: http://lattes.cnpq.br/7355685961127056
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
