Finding and Searching Files

Searching with grep

The grep command is commonly used in UNIX to filter a file or input, line by line, against a pattern. Patterns can be complex and use regular expressions, but most of the time wildcards are sufficient.

grep [OPTIONS] PATTERN FILENAME

Example

The -i option stands for “ignore case.”

$grep -i Unix intro_basic-unix.txt

Grep is frequently used with wildcards and pipes.

$grep -i write *f90
$grep weight: *md | grep 100

Example

How many sequences are in a FASTA-formatted file? Each sequence record in a FASTA file has one line of description that always starts with >, followed by multiple lines of the sequence itself. Each sequence record ends when the next line starts with >.

$grep -c '>' sequences.fasta

The -c option returns the number of lines containing the pattern. Please be sure to include the quotes around the > or the shell will interpret it as a redirection.

A Handy Trick

To find all occurrences of a pattern in all files in a directory, use grep -r.

$grep -r "print" python_programs

Be careful with the pattern for a recursive search, or the output can be excessive.

Finding Files by Name

The find command can locate a file if you cannot remember its directory. It can take wildcards, in which case it is best to use quotes around the name pattern.

$find . -name 2col.txt
./shakespeare/2col.txt
$find . -name "people*"
./data/people.txt

The period . tells find to start at the current working directory.

Find has many options to locate files by name, type, date, and others. See here for examples.