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update read.beast #48

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merged 3 commits into from
Mar 10, 2021
Merged

update read.beast #48

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cb4cf22
update read.beast
xiangpin Mar 8, 2021
2938b4d
better parse single value to single key in stats infor of beast
xiangpin Mar 9, 2021
bf379f9
remove elements before = in values of annotation
xiangpin Mar 10, 2021
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30 changes: 24 additions & 6 deletions R/beast.R
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Original file line number Diff line number Diff line change
Expand Up @@ -175,8 +175,16 @@ read.stats_beast_internal <- function(beast, tree) {
## BEAST output
stats <- strsplit(tree, ":") %>% unlist
}

names(stats) <- node

# check whether the stats info is after edge length or not.
if (!all(grepl("]$", stats) || grepl("];$", stats))){
# t1:0.04[&mutation="test1"]
stats <- sub("].*", "", stats)
names(stats) <- c(rep(node[1],2),node[-c(1,length(node))])
}else{
# t1[&mutation="test1"]:0.04
names(stats) <- node
}

stats <- stats[grep("\\[", stats)]
stats <- sub("[^\\[]*\\[", "", stats)
Expand All @@ -188,15 +196,25 @@ read.stats_beast_internal <- function(beast, tree) {
stats2 <- lapply(seq_along(stats), function(i) {
x <- stats[[i]]
y <- unlist(strsplit(x, ","))
sidx <- grep("=\\{", y)
eidx <- grep("\\}$", y)

# the stats information does not has always {}
#sidx <- grep("=\\{", y)
#eidx <- grep("\\}$", y)
# [&mutation="test1,test2",rate=80,90]
sidx1 <- grep("=", y)
eidx1 <- sidx1 - 1
eidx1 <- c(eidx1[-1], length(y))
# for better parsing [&mutation="test",name="A"] single value to key.
sidx <- sidx1[!(sidx1==eidx1)]
eidx <- eidx1[!(sidx1==eidx1)]

flag <- FALSE
if (length(sidx) > 0) {
flag <- TRUE
SETS <- lapply(seq_along(sidx), function(k) {
p <- y[sidx[k]:eidx[k]]
gsub(".*=\\{", "", p) %>% gsub("\\}$", "", .)
gsub(".*=\\{", "", p) %>%
gsub("\\}$", "", .) %>%
gsub(".*=", "", .)
})
names(SETS) <- gsub("=.*", "", y[sidx])

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