Mainly archiving this for the benefit of future-me.

The problem

Given an a list of files where I want to search and replace all whole-word occurences of reference_name with chromosome

grep -rw reference_name * | head
load/formats.yaml:        chrom:   reference_name
load/load-functions.R:    df1$reference_name = gsub('chr', '', df1$reference_name)
load/load-helper.R:    new_features$reference_name = 'unknown'
load/load-helper.R:    new_features$reference_name = 'unknown'
# .. hundreds of other occurences

The solution

sed -i 's/\<$string_to_search\>/$REPLACE_WITH/g' `grep -rw -l $string_to_search *`


  • -l is for giving location of file only (not the entire output) [Link]
  • -w is for whole word occurences only
  • \<$string_to_search\> is the whole word occurence search equivalent in vim