r语言 - 在数据框中使用正则表达式提取部分列

Question

我需要帮助，以便在R数据框架上使用正则表达式。

数据框架:

Names
1                                                                                                [NW_019417116.1_2_3-HSPs_-__Canis_glabripennis]
2                                  [scaffold_29690_2-HSPs_-__Lopus_eremicus,scaffold_3037_+__Pig_sd,scaffold_144501_556-844_+__Lopus_eremicus]
3 [UDEW01029642.1_1-357_+__Falis_catus,scaffold_100683_331-631_+__Pig_sud,scaffold_209026_2-HSPs_+__Pig_sud,scaffold_220973_58-331_+__Pig_sud]
4                                                                       [scaffold_27087_+__Falis_catus,scaffold_77874_2-HSPs_-__Ratus_griseus]

和在df$Names中，我想为HSPs的行提取两个部分(部分具有物种名称，看起来像(__Content_content):

例如在scaffold_77874_2-HSPs_-__Ratus_griseus中，这在Ratus_griseus中和脚手架部分，在scaffold_77874_2-HSPs_-__Ratus_griseus中，在scaffold_77874部分

因此，我创建了两个新列，并应该得到所需的输出:

Names                                                                                                                                         Specie_name         Scaffold_name
[NW_019417116.1_2_3-HSPs_-__Canis_glabripennis]                                                                                               Canis_glabripennis  NW_019417116.1_2
[scaffold_29690_2-HSPs_-__Lopus_eremicus,scaffold_3037_+__Pig_sd,scaffold_144501_556-844_+__Lopus_eremicus]                                   Lopus_eremicus      UDEW01029642.1
[UDEW01029642.1_1-357_+__Falis_catus,scaffold_100683_331-631_+__Pig_sud,scaffold_209026_2-HSPs_+__Pig_sud,scaffold_220973_58-331_+__Pig_sud]  Pig_sud             scaffold_209026
[scaffold_27087_+__Falis_catus,scaffold_77874_2-HSPs_-__Ratus_griseus]                                                                        Rattus_griseus      scaffold_77874

So far I try:

df %>%
mutate(Scaffold_name = str_match(Names, regex(',(.*)_\d+-HSPs'))[, 2], 
Specie_name = str_extract(Names, ',(.*)_\d+-HSPs_.__.*,|,(.*)_\d+-HSPs_.__.*]|\[*.[^,]*_\d+-HSPs_.__.*\]'),
Specie_name = gsub(',','',Specie_name),
Specie_name = gsub(']','',Specie_name),
Specie_name = gsub('\[','',Specie_name),
Specie_name = gsub('.*__','',Specie_name)
) 

这里是数据

structure(list(Names = structure(c(1L, 3L, 4L, 2L), .Label = c("[NW_019417116.1_3-HSPs_-__Canis_glabripennis]", 
"[scaffold_27087_+__Falis_catus,scaffold_77874_2-HSPs_-__Ratus_griseus]", 
"[scaffold_29690_2-HSPs_-__Lopus_eremicus,scaffold_3037_+__Pig_sd,scaffold_144501_556-844_+__Lopus_eremicus]", 
"[UDEW01029642.1_1-357_+__Falis_catus,scaffold_100683_331-631_+__Pig_sud,scaffold_209026_2-HSPs_+__Pig_sud,scaffold_220973_58-331_+__Pig_sud]"
), class = "factor")), class = "data.frame", row.names = c(NA, 
-4L))

Answer 1

我们可以使用separate_rows在,处拆分'Names'，然后通过删除[和]来清理'Names'列，separate通过在-[-+]__处拆分'Names'成两列

library(dplyr)
library(tidyr)
library(stringr)
df %>% 
mutate(Names = as.character(Names)) %>%      
separate_rows(Names, sep=",") %>% 
mutate(Names = str_remove_all(Names, "\[|\]")) %>% 
filter(str_detect(Names, "HSPs")) %>%
separate(Names, into = c('Scaffold_name', "Specie_name"),
sep = "_[-+]__", remove = FALSE) %>% 
mutate(Scaffold_name = str_remove(Scaffold_name, "-HSPs"))

---

或者我们可以通过直接提取子字符串来避免filter/separate_rows，然后再提取separate

df %>%
mutate(sub_name = str_extract(Names, "[[:alnum:]._]+-HSPs[^,]+")) %>% 
separate(sub_name, into = c('Scaffold_name', 'Specie_name'),
sep='-HSPs_[-+]__') %>%
mutate(Specie_name = str_remove(Specie_name, "\]"))

与产出

                                                                 #Names
#1                                                                                                [NW_019417116.1_3-HSPs_-__Canis_glabripennis]
#2                                  [scaffold_29690_2-HSPs_-__Lopus_eremicus,scaffold_3037_+__Pig_sd,scaffold_144501_556-844_+__Lopus_eremicus]
#3 [UDEW01029642.1_1-357_+__Falis_catus,scaffold_100683_331-631_+__Pig_sud,scaffold_209026_2-HSPs_+__Pig_sud,scaffold_220973_58-331_+__Pig_sud]
#4                                                                       [scaffold_27087_+__Falis_catus,scaffold_77874_2-HSPs_-__Ratus_griseus]
#      Scaffold_name        Specie_name
#1  NW_019417116.1_3 Canis_glabripennis
#2  scaffold_29690_2     Lopus_eremicus
#3 scaffold_209026_2            Pig_sud
#4  scaffold_77874_2      Ratus_griseus