我花了很多时间试图解决这个问题，但没有成功。
我有一个data. frame，其中包含一个包含可变长度字符串的列。data.frame如下所示：
Taxa <- as.character(c("cellularorganisms(norank)_Bacteria(superkingdom)_Actinobacteria(phylum)","cellularorganisms(norank)_Bacteria(superkingdom)_Proteobacteria(phylum)_Gammaproteobacteria(class)_Enterobacteriales(order)_Enterobacteriaceae(family)","cellularorganisms(norank)_Bacteria(superkingdom)_Proteobacteria(phylum)_Gammaproteobacteria(class)_Enterobacteriales(order)","cellularorganisms(norank)_Bacteria(superkingdom)_Proteobacteria(phylum)_Gammaproteobacteria(class)_Enterobacteriales(order)_Enterobacteriaceae(family)_Klebsiella(genus)","cellularorganisms(norank)_Bacteria(superkingdom)_Proteobacteria(phylum)_Gammaproteobacteria(class)_Enterobacteriales(order)_Enterobacteriaceae(family)_Klebsiella(genus)_Klebsiellapneumoniae(species)","cellularorganisms(norank)_Bacteria(superkingdom)_Firmicutes(phylum)_Clostridia(class)_Clostridiales(order)","cellularorganisms(norank)_Bacteria(superkingdom)_Firmicutes(phylum)_Clostridia(class)","cellularorganisms(norank)_Bacteria(superkingdom)_Firmicutes(phylum)_Clostridia(class)_Clostridiales(order)_Clostridiaceae(family)","cellularorganisms(norank)_Bacteria(superkingdom)_Firmicutes(phylum)_Clostridia(class)_Clostridiales(order)_Clostridiaceae(family)_Clostridium(genus)","cellularorganisms(norank)_Bacteria(superkingdom)_Firmicutes(phylum)_Clostridia(class)_Clostridiales(order)_Clostridiaceae(family)_Clostridium(genus)_Clostridiumbotulinum(species)","cellularorganisms(norank)_Bacteria(superkingdom)_Firmicutes(phylum)_Clostridia(class)_Clostridiales(order)_Clostridiaceae(family)_Clostridium(genus)_Clostridiumbotulinum(species)_ClostridiumbotulinumCDC66177(strain)","cellularorganisms(norank)_Bacteria(superkingdom)_Actinobacteria(phylum)_Actinobacteria(class)_Actinobacteridae(subclass)_Actinomycetales(order)_Micrococcineae(suborder)","cellularorganisms(norank)_Bacteria(superkingdom)_Actinobacteria(phylum)_Actinobacteria(class)_Actinobacteridae(subclass)_Actinomycetales(order)_Micrococcineae(suborder)_Microbacteriaceae(family)","cellularorganisms(norank)_Bacteria(superkingdom)_Actinobacteria(phylum)_Actinobacteria(class)_Actinobacteridae(subclass)_Actinomycetales(order)_Micrococcineae(suborder)_Microbacteriaceae(family)_Microbacterium(genus)","cellularorganisms(norank)_Bacteria(superkingdom)_Actinobacteria(phylum)_Actinobacteria(class)_Actinobacteridae(subclass)_Actinomycetales(order)_Micrococcineae(suborder)_Microbacteriaceae(family)_Microbacterium(genus)_Microbacteriumlaevaniformans(species)_MicrobacteriumlaevaniformansOR221(strain)"))
Percent <- c("0.000400","0.006800","0.005034","0.001760","0.000000","0.000000","0.344400","0.000000","0.000000","0.000000","0.006500","0.002819","0.000487","0.000000","0.001090")
Test <- data.frame(Percent, Taxa)
Test$Taxa <- as.character(Test$Taxa)
我可以将下划线上的这些字符串子集为不相等长度的列表：
NewDF <- strsplit(Test$Taxa, "_", fixed=TRUE)
但是我不知道如何将这个解析的输出格式化为可用的结构。
每个解析的部分有两个组件，一个描述符和一个分类级别（即细菌（超级王国）是描述符细菌和分类级别的超级王国。
我想做的是获取这个解析后的输出，并填充一个具有以下列标题（norank、超级王国、门、类、顺序、科、属、种、株）的data. frame。输出需要跳过上面列表中未包含的分类级别（例如，在class和order之间有具有分类级别子类的行，我需要删除子类）。
此外，如果一行停在特定的分类级别并且仍有未填充的列，则应将它们设置为NA（即第一行以门结束，因此类、顺序、家族等应为NA）。
最终输出应如下所示：
norank superkingdom phylum class order family genus species strain
1 cellularorganisms(norank) Bacteria(superkingdom) Actinobacteria(phylum) <NA> <NA> <NA> <NA> <NA> <NA>
2 cellularorganisms(norank) Bacteria(superkingdom) Proteobacteria(phylum) Gammaproteobacteria(class) Enterobacteriales(order) Enterobacteriaceae(family) <NA> <NA> <NA>
3 cellularorganisms(norank) Bacteria(superkingdom) Proteobacteria(phylum) Gammaproteobacteria(class) Enterobacteriales(order) <NA> <NA> <NA> <NA>
4 cellularorganisms(norank) Bacteria(superkingdom) Proteobacteria(phylum) Gammaproteobacteria(class) Enterobacteriales(order) Enterobacteriaceae(family) Klebsiella(genus) <NA>
5 cellularorganisms(norank) Bacteria(superkingdom) Proteobacteria(phylum) Gammaproteobacteria(class) Enterobacteriales(order) Enterobacteriaceae(family) Klebsiella(genus) Klebsiellapneumoniae(species) <NA>
6 cellularorganisms(norank) Bacteria(superkingdom) Firmicutes(phylum) Clostridia(class) Clostridiales(order) <NA> <NA> <NA> <NA>
7 cellularorganisms(norank) Bacteria(superkingdom) Firmicutes(phylum) Clostridia(class) <NA> <NA> <NA> <NA> <NA>
8 cellularorganisms(norank) Bacteria(superkingdom) Firmicutes(phylum) Clostridia(class) Clostridiales(order) Clostridiaceae(family) <NA> <NA> <NA>
9 cellularorganisms(norank) Bacteria(superkingdom) Firmicutes(phylum) Clostridia(class) Clostridiales(order) Clostridiaceae(family) Clostridium(genus) <NA> <NA>
10 cellularorganisms(norank) Bacteria(superkingdom) Firmicutes(phylum) Clostridia(class) Clostridiales(order) Clostridiaceae(family) Clostridium(genus) Clostridiumbotulinum(species) <NA>
11 cellularorganisms(norank) Bacteria(superkingdom) Firmicutes(phylum) Clostridia(class) Clostridiales(order) Clostridiaceae(family) Clostridium(genus) Clostridiumbotulinum(species) ClostridiumbotulinumCDC66177(strain)
12 cellularorganisms(norank) Bacteria(superkingdom) Actinobacteria(phylum) Actinobacteria(class) Actinomycetales(order) <NA> <NA> <NA> <NA>
13 cellularorganisms(norank) Bacteria(superkingdom) Actinobacteria(phylum) Actinobacteria(class) Actinomycetales(order) Microbacteriaceae(family) <NA> <NA> <NA>
14 cellularorganisms(norank) Bacteria(superkingdom) Actinobacteria(phylum) Actinobacteria(class) Actinomycetales(order) Microbacteriaceae(family) Microbacterium(genus) <NA> <NA>
15 cellularorganisms(norank) Bacteria(superkingdom) Actinobacteria(phylum) Actinobacteria(class) Actinomycetales(order) Microbacteriaceae(family) Microbacterium(genus) Microbacteriumlaevaniformans(species) MicrobacteriumlaevaniformansOR221(strain)
您可以尝试通过将小data. frame列表编译成一个df来做到这一点
library(dplyr)
NewDF <-
lapply(strsplit(Test$Taxa, "_", fixed=TRUE),
function(x)
{
vars <- lapply(x, function(y)
{
m <- regexec("\\((.+?)\\)",y)
regmatches(y,m)[[1]][2]
})
vals <- as.list( x )
names(vals) <- unlist(vars)
data.frame( vals,
stringsAsFactors = FALSE )
}) %>% rbind_all
这给了我你想要的结果（也有好看的变量名）
