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##' parse tabular output of MEGA
##'
##'
##' @title read.mega_tabular
##' @param file MEGA tabular file
##' @return treedata object
##' @export
##' @author Guangchuang Yu
read.mega_tabular <- function(file) {
## output of MEGA 7 has "datafile=X", while output of MEGA X may not
skip <- ifelse(grepl("datafile=",
suppressMessages(scan(file, n = 1, what = character()))),
1, 0)
d <- suppressMessages(vroom::vroom(file, skip = skip))
d1 <- d[,c('NodeId','Des1')] %>% dplyr::rename(child=.data$Des1)
d2 <- d[,c('NodeId','Des2')] %>% dplyr::rename(child=.data$Des2)
dd <- dplyr::bind_rows(d1, d2) %>% dplyr::filter(child != '-')
d <- dplyr::mutate(d, label = as.character(.data$NodeId))
obj <- as.phylo(dd) %>% as_tibble %>%
dplyr::full_join(d, by='label') %>%
dplyr::mutate(label=sub("^-$", "", .data$NodeLabel)) %>%
dplyr::select(-c('NodeLabel', 'NodeId', 'Des1', 'Des2')) %>%
as.treedata
obj@file <- filename(file)
return(obj)
}
##' @rdname beast-parser
##' @export
read.mega <- read.beast
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