英文:
How to replace specific string within string using dictionary from data frame?
问题
listn2 <- stringr::str_replace_all(string = listn,pattern = ddf$old,replacement = ddf$new)
英文:
I have a dictionary of bipartite taxonomic names (each composed of two words) in the form of a data frame (ddf). Where there are columns with old (ddf$old) and new (ddf$new) names. I would like to find & replace the old names with the new names in a list of strings (listn). However, the taxonomic names are a part of the string. Some old names may occur more than once and some may never appear in the list. The old names proceed with a string of different lengths and sometimes are followed by an additional string.
#sample list, the real has >300000 entrieslistn <- c("AB001440.1.1538 Pseudomonas coronafaciens pv. atropurpurea", "HG530070.1.1349 Trueperella pyogenes","ET631036.837.2346 Jonquetella anthropi", "AB001448.1.1538 Pseudomonas savastanoi pv. phaseolicola","HG530249.1.1462 Paucibacter toxinivorans", "HG530235.1.1493 Paucibacter toxinivorans","AB001781.1.1507 Chlamydia psittaci", "AB001785.1.1507 Chlamydia felis","AB001804.1.1507 Chlamydia psittaci", "AB001794.1.1507 Chlamydia psittaci")#sample dictionary, the real one has >400 entriesddf <- data.frame(old = c("Lactobacillus casei", "Trueperella pyogenes", "Pseudomonas savastanoi"),new = c("Newbacillus casei", "Newperella pyogenes", "Newudomonas savastanoi"))
I tried:
listn2 <- stringr::str_replace_all(string = listn,pattern = ddf$old,replacement = ddf$new)list2 <- gsub(ddf$old, ddf$new, listn)
None of the methods worked. I expect to have two specific words replaced by another two words based on the dictionary from the data frame. The old and new names are of different lengths.
I tried ChatGPT, but it wasn't smart enough and provided such a script:
# Sample input dataselected_strings <- c("John likes apples", "Mary eats bananas", "David enjoys grapes")dictionary <- data.frame(old_name = c("John", "Mary", "David"),new_name = c("Peter", "Alice", "Michael"),stringsAsFactors = FALSE)# Function to replace bipartite names within selected stringsreplace_names <- function(strings, dictionary) {# Split the strings into individual wordswords <- unlist(strsplit(strings, " "))# Replace the names using the dictionaryreplaced_words <- wordsfor (i in seq_len(nrow(dictionary))) {replaced_words[words == dictionary$old_name[i]] <- dictionary$new_name[i]}# Reconstruct the modified stringsmodified_strings <- sapply(strsplit(strings, " "), function(x) paste(replaced_words[x], collapse = " "))return(modified_strings)}# Call the function to replace names within selected stringsmodified_strings <- replace_names(selected_strings, dictionary)# Print the modified stringsprint(modified_strings)
答案1
得分: 1
你可以使用一个命名的替换：
library(tidyverse)str_replace_all(listn, deframe(ddf))
同样可以使用以下方式：
str_replace_all(listn, setNames(ddf$new, ddf$old))
英文:
You can use a named replacement:
library(tidyverse)str_replace_all(listn, deframe(ddf))[1] "AB001440.1.1538 Pseudomonas coronafaciens pv. atropurpurea"[2] "HG530070.1.1349 Newperella pyogenes"[3] "ET631036.837.2346 Jonquetella anthropi"[4] "AB001448.1.1538 Newudomonas savastanoi pv. phaseolicola"[5] "HG530249.1.1462 Paucibacter toxinivorans"[6] "HG530235.1.1493 Paucibacter toxinivorans"[7] "AB001781.1.1507 Chlamydia psittaci"[8] "AB001785.1.1507 Chlamydia felis"[9] "AB001804.1.1507 Chlamydia psittaci"[10] "AB001794.1.1507 Chlamydia psittaci"
same as:
str_replace_all(listn, setNames(ddf$new, ddf$old))
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