No tip label for one of the tips
lpipes opened this issue · comments
Hi, I printed out the tip labels (tree$tip.label) however one of the tips doesn't have a label:
I used
write.table(file="tips.txt",sep="\t",quote=F,as.data.frame(tree$tip.label))
In tips.txt:
12144628 EPI_ISL_3025220
12144629 EPI_ISL_2959021
12144630 EPI_ISL_16960747
12144631
12144632 EPI_ISL_454951
12144633 EPI_ISL_450458
12144634 EPI_ISL_476780
Hi, How did you get tree into R? It could have been badely processed by ape, or if it came from a Newick file, the latter may have been wrong.
I just used read.tree() to get the tree into R. The Newick file was a file written by write.tree() after I had used multi2di and collapse.singles().
Can you post the file here?
Unfortunately, the file is 64MB gzipped and only 25MB is allowed. Is there another way I can send it?
I uploaded it on Google drive: https://drive.google.com/file/d/1fxQ12_NTXu-gLH60k5TpZoOc_1W7Ig0y/view?usp=sharing
It seems the Newick file has a problem: one tip label has been replaced by a 'newline' (\n):
...:0):0):0,(EPI_ISL_16960747:0,\n:0):0):0):0)...
Here's the R code to help diagnose this:
fl <- "global.out.tree" # after unzipping
library(ape)
tree <- read.tree(fl)
nc <- nchar(tree$tip.label)
zero.tiplab <- nc == 0
sum(zero.tiplab) # how many zero-length labels?
i <- which(zero.tiplab)
w <- which(tree$edge[, 2] == i)
anc <- tree$edge[w, 1]
j <- which(tree$edge[, 1] == anc)
tree$edge[j, ]
tree$tip.label[12144630] # <- this is the sister of ""
tree$tip.label[12144631] # ""
x <- readBin(fl, raw(), file.size(fl))
xchar <- rawToChar(x)
sister <- tree$tip.label[12144630]
gregexpr(sister, xchar)
## use the last output to do:
substr(xchar, 272732648 - 10, 272732648 + 31)