Finding Things


  • Questions

    • How to download and extract files from the internet?

    • How can we find files in complex folders?

    • How can we find lines in files?

  • Keypoints

    • grep and find can be used to find files

    • grep can also be used to search in files

Instructor note

  • Demo/teaching: 15 min

  • Exercise: 15 min

A critical skill for working on to have the skills to find files and folders (again).


To get the files and folder structure for the following exercises we will use a combination of two often used tools:

  1. wget URL will download whatever is specified by URL and save it in the current folder.

  2. tar is used for packing and unpacking archives with file suffixes like .tar, .tar.gz or .tar.bz2. It is infamous for its confusing parameters.

$ wget
$ tar xzvf finding.tar.gz

Finding files in folders with find

You should now have a folder named test_data in your current directory containing a bunch of files and folders with random names and different file types.

Now we will try to find a couple of different files in this mess. Let’s start a file called output.txt which has to be in one of the subfolders. Our tools is fittingly called find and is available on all Unix and Linux machines. The general syntax is quite simple


but if we look into its help file using man find, we see that there are tons of parameters and options available.

Based on file name

In our case, we know the folder in which to look (the ‘STARTING_POINT’) and the exact name, so the command becomes:

$ find test_data -name output.txt

If, for some reason we are not sure about the capitalization of our file (was it ‘output.txt’, ‘Output.txt’, ‘OUTPUT.txt’ or something else), we can use -iname instead. This way we ignore the case of search term

$ find test_data -iname output.txt

Let’s imagine that we forgot the name of a data file we want to use but we remember it is a .csv file. We could look through each folder separately or try out all names with a .csv suffix, we can think off. Instead we can use find in combination with wildcard characters (see here for more information). The two most useful wildcards are the asterisk (*) and the question mark (?). The asterisk matches zero or more characters while the question mark represents any single character.

So if we want to list all .csv files, we can use the asterisk like this:

$ find test_data -iname '*.csv'

We use -iname here to also match .CSV files (we don’t want to miss them unintentionally). The quotation marks make sure that the *.csv is interpreted by find and not the shell (bash) itself.

Based on other attributes

find can not only be used to look for files based on their name but also on other properties like file size or access/modification date. This can be useful to display only files which have been changed or created in the last minutes or hours.

For example, let’s create a new empty file with

$ touch test_data/new_file.txt

This file is now much newer than the other files in the folder and we can find it with the either the -amin or -mmin option, depending if we are looking for access or modification time, respectively.

$ find test_data -mmin -10

We will get all files or folders that have been modified (in our case, have been created) less than 10 min ago. By contrast -mmin +10 would show all files that have been modified more than 10 min ago.

Another property, that is sometimes useful for differentiating files, is their size. If we want to see all files in our test_data directory larger than 100 kB we can use

$ find test_data -size +100k

Other possible input options are for example -1M (smaller than 1 MB) or +2G (larger than 2 GB).

Combining attributes

To unlock find’s full potential, it is possible to combine different attribute to search for files very precisely. If we for example want to find all .csv files with a size of greater than 200 kB we can use:

$ find test_data -name '*.csv' -size +200k

Finding lines in a file with grep

While findis useful for finding files based on their names and other parameters, grep let’s us find things within files. Basic usage (there are a lot of options for more clever things, see the man page man grep) uses the syntax grep whatToFind fileToSearch.

We got a list of genes from a colleague, we want to analyse for a project. First let’s find the list with find and have a look at its layout with head.

$ find test_data -name 'genelist.tsv'
$ head -n5 test_data/genelist.tsv

We see that the file contains genes organised in three columns, the last describing the organism. Assuming we first want to list all genes from rats, we can use grep like this:

$ grep rat test_data/genelist.tsv

This return one result. But from our colleague’s email we know that there should be two rat genes, so we try the -i option to ignore capitalization:

$ grep -i rat test_data/genelist.tsv

This time we get both genes as result.

We remembered these genes from a conversation with another colleague. Fortunately we wrote down some notes. But where is the files with the notes? It must be in our folder. So let’s look for the gene name in all files in the folder ‘test_data’ using the -r option of grep:

$ grep -r Hsd17b10 test_data -C 1 -n

As expected, this returns the gene in ‘genelist.tsv’ but the note file we were looking for. -n shows the line number and -C 1 provides us with some context by displaying one line before and after the line containing our search term.


Exercise (15 min)

  1. We not only forgot where we saved the output file output.txt to but also the figure we plotted. How can you find the file graph.jpg? How do we look for this file only in the folder experiment1 and its subfolders?

  2. Now we want to find a plot we saved somewhere but we don’t remember which file format we used (.jpg, .bmp, .png or something else). How could you find a file with the name ‘plot’ but unknown suffix?

  3. Let’s assume that we can’t remember if our our output files are of type .jpg or .JPG but we know that it is larger than 500 kB. How can we find it?

  4. The notes file also contained the gene ‘AtFDH1’ that might be interesting. From which organism is that gene in the ‘genelist.tsv’ file?

  5. How can we find the file containing the sequence of gene ‘Hsd17b10’? It is saved somewhere in our folder but not properly labeled?