Use grep to find text in a note

Search for specific patterns in your files

Lab notebooks are great for capturing your actions and reflections in a timestamped manner, but who remembers the date when you did that thing that you want to do again today? To find a note from about a month ago, when I compared the bowtie2 and bwa aligners, I can search for the two terms using grep.

Move into the folder you want to search. My folder is called ‘notes’.

cd notes/

Search this folder . for files with the suffix .md. Print the output and pipe them as arguments to grep. As the grep man pages say, grep searches the named input files for lines containing a match to the given pattern. In the case below, the pattern is bowtie2.

find . -name '*.md' -print | xargs grep 'bowtie2'

By default, find looks in the directory you are currently in, so you don’t need the .. Also, by default, find prints the names of the directories and files inside them, so you don’t need -print. If you don’t want to specify a file extension and do want to look in all files, then you don’t need -name.

You can look for the presence of multiple words in a file with the following:

find | xargs grep -e 'bowtie2' -e 'bwa'

grep

grep 'pattern'

• grep stands for ‘gnu regular expressions’
• grep searches input files for matches to the argument pattern (in quotes)
• in the case above, the pattern is ‘bowtie2’

grep 'bowtie[^2]'

• returns all files that have the word ‘bowtie’, but not ^ those that have ‘bowtie2'
• the not ^ symbol applies to all letters within the brackets
• e.g. you could write [^234] so file names with 2, 3, or 4 after ‘bowtie’ would NOT be returned
• grep is not “hungry”, meaning not all of the characters in the strings it reviews have be accounted for in the string it is searching for
• when grep finds a match in a line, it copies the line to standard output
• mv cannot process the output of grep, thus xargs is used above

grep --version

• grep comes with OSX command line utilities
• more updated versions of grep can be installed with Homebrew (not necessary): brew install grep