Splitting strings containing multiple delimiters in R

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I have a vector tissue which contains strings delimited by multiple characters. The constituent strings of the vector belong broadly to four classes:

  1. Strings which only consist of term(s) (e.g. Thymus Thyroid) separated by ,

  2. Strings which contain identifier(s) (e.g. ECO:0000313|RefSeq:XP_014046664.1) ending with }, followed by term(s) separated by ,

  3. Strings which contain a term followed by identifier(s)

  4. Strings which contain a term followed by an identifier and then term(s) separated by ,

    tissue <- c("Head kidney,Thymus,Thyroid,", 
            "Red blood cell,", 
            "ECO:0000313|RefSeq:XP_014046664.1},Muscle,",
            "ECO:0000313|RefSeq:XP_016683349.1},ECO:0000313|RefSeq:XP_016683354.1},Leaf,", 
            "ECO:0000313|RefSeq:XP_014023833.1},Head kidney,Muscle,White muscle,",
            "Blood,ECO:0000313|RefSeq:XP_017326031.1},",
            "Spleen,ECO:0000313|RefSeq:XP_010844217.1},ECO:0000313|RefSeq:XP_010844218.1},",
            "Brain,ECO:0000313|RefSeq:XP_014030244.1},Head kidney,Muscle,Spleen,White muscle,")

For strings belonging to category 1, I could split the terms using a simple strsplit() function

unlist(strsplit("Head kidney,Thymus,Thyroid,", ","))
[1] "Head kidney" "Thymus"      "Thyroid" 

unlist(strsplit("Red blood cell,", ","))
[1] "Red blood cell"

For strings belonging to category 2, this is what I came up with and it works fine

unlist(strsplit(sub('.*\\},', "", "ECO:0000313|RefSeq:XP_014046664.1},Muscle,"), ","))
[1] "Muscle"

unlist(strsplit(sub('.*\\},', "", "ECO:0000313|RefSeq:XP_016683349.1},ECO:0000313|RefSeq:XP_016683354.1},Leaf,"), ","))
[1] "Leaf"

unlist(strsplit(sub('.*\\},', "", "ECO:0000313|RefSeq:XP_014023833.1},Head kidney,Muscle,White muscle,"), ","))
[1] "Head kidney"  "Muscle"       "White muscle"

For strings belonging to category 3, this worked for me

sub(',ECO:.*', "", "Blood,ECO:0000313|RefSeq:XP_017326031.1},")
[1] "Blood"

sub(',ECO:.*', "", "Spleen,ECO:0000313|RefSeq:XP_010844217.1},ECO:0000313|RefSeq:XP_010844218.1},")
[1] "Spleen"

For category 4, this is what I tried and it works fine

unlist(strsplit(sub(',ECO:.*},', ",", "Brain,ECO:0000313|RefSeq:XP_014030244.1},Head kidney,Muscle,Spleen,White muscle,"), ","))
[1] "Brain"        "Head kidney"  "Muscle"       "Spleen"       "White muscle"

I'm looking for a solution, a single regex if possible, which can handle all these conditions and can be used directly on the vector.

r regex string
2 Answers

We may remove some of the substring and then use strsplit

library(stringr)
lapply(strsplit(str_remove_all(tissue, "ECO:[^\\}]+\\}"), ","), 
     function(x) x[nzchar(x)])

-output

[[1]]
[1] "Head kidney" "Thymus"      "Thyroid"    

[[2]]
[1] "Red blood cell"

[[3]]
[1] "Muscle"

[[4]]
[1] "Leaf"

[[5]]
[1] "Head kidney"  "Muscle"       "White muscle"

[[6]]
[1] "Blood"

[[7]]
[1] "Spleen"

[[8]]
[1] "Brain"        "Head kidney"  "Muscle"       "Spleen"       "White muscle"

Or with a tidyverse work flow

library(dplyr)
library(tidyr)
str_remove_all(tissue, "ECO:[^\\}]+\\}") %>% 
  trimws(whitespace = ",+") %>%
  str_replace_all(',{2,}', ",") %>% 
  tibble(col1 = .) %>% 
  tidyr::separate(col1, into = str_c('V', 
    seq(max(str_count(.$col1, ",")) + 1)), sep = ",", fill = "right")

-output

# A tibble: 8 × 5
  V1             V2          V3           V4     V5          
  <chr>          <chr>       <chr>        <chr>  <chr>       
1 Head kidney    Thymus      Thyroid      <NA>   <NA>        
2 Red blood cell <NA>        <NA>         <NA>   <NA>        
3 Muscle         <NA>        <NA>         <NA>   <NA>        
4 Leaf           <NA>        <NA>         <NA>   <NA>        
5 Head kidney    Muscle      White muscle <NA>   <NA>        
6 Blood          <NA>        <NA>         <NA>   <NA>        
7 Spleen         <NA>        <NA>         <NA>   <NA>        
8 Brain          Head kidney Muscle       Spleen White muscle

Or using only base R

read.csv(text = gsub(",{2,}", ",", trimws(gsub("ECO:[^\\}]+\\}", 
    "", tissue), whitespace = ",+")), header = FALSE, fill = TRUE, sep=",")
user_37322710

How about:

library(stringr)

x <- str_remove(unlist(str_match_all(tissue, '(.*?)(?=\\,)')), '^ECO.*')
unique(x[x != ""])

[1] "Head kidney"    "Thymus"         "Thyroid"        "Red blood cell"
 [5] "Muscle"         "Leaf"           "White muscle"   "Blood"         
 [9] "Spleen"         "Brain"
user_133216470
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