Working with Files and Directories

Overview

Questions

• How can I view and search file contents?
• How can I create, copy and delete files and directories?
• How can I control who has permission to modify a file?
• How can I repeat recently used commands?

Objectives

• View, search within, copy, move, and rename files. Create new directories.
• Use wildcards (*) to perform operations on multiple files.
• Make a file read only
• Use the history command to view and repeat recently used commands.

Working with Files

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Our data set: FASTQ files

Now that we know how to navigate around our directory structure, lets start working with our sequencing files. We did a sequencing experiment and have two results files, which are stored in our data directory.

Wildcards

Navigate to your data directory.

BASH

$ cd ~/pan_workshop/data

We are interested in looking at the FASTA files in this directory. We can list all files with the .fastq extension using the command:

BASH

$ ls */*.gbk

OUTPUT

agalactiae_18RS21/Streptococcus_agalactiae_18RS21.gbk  agalactiae_H36B/Streptococcus_agalactiae_H36B.gbk

The * character is a special type of character called a wildcard, which can be used to represent any number of any type of character. Thus, *.gbk matches every file that ends with .gbk.

Command History

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If you want to repeat a command that you’ve run recently, you can access previous commands using the up arrow on your keyboard to go back to the most recent command. Likewise, the down arrow takes you forward in the command history.

A few more useful shortcuts:

• Ctrl+C will cancel the command you are writing, and give you a fresh prompt.
• Ctrl+R will do a reverse-search through your command history. This is very useful.
• Ctrl+L or the clear command will clear your screen.

You can also review your recent commands with the history command, by entering:

BASH

$ history

to see a numbered list of recent commands. You can reuse one of these commands directly by referring to the number of that command.

For example, if your history looked like this:

OUTPUT

479  ls *
480  ls /usr/bin/*.sh
481  ls *.gbk

then you could repeat command #481 by entering:

BASH

$ !481

Type ! (exclamation point) and then the number of the command from your history. You will be glad you learned this when you need to re-run very complicated commands.

Examining Files

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We now know how to switch directories, run programs, and look at the contents of directories, but how do we look at the contents of files?

One way to examine a file is to print out all of the contents using the program cat.

$ cat filename

cat is a terrific program, but when the file is really big (as the files we have), it can be annoying to use. The program, less, is useful for this case. less opens the file as read only, and lets you navigate through it. The navigation commands are identical to the man program.

Enter the following command:

BASH

$  cd ~/pan_workshop/data/agalactiae_18RS21
$ ls

OUTPUT

Streptococcus_agalactiae_18RS21.fna  Streptococcus_agalactiae_18RS21.gbk

BASH

$ less Streptococcus_agalactiae_18RS21.gbk

Some navigation commands in less

key	action
Space	to go forward
b	to go backward
g	to go to the beginning
G	to go to the end
q	to quit

less also gives you a way of searching through files. Use the “/” key to begin a search. Enter the word you would like to search for and press enter. The screen will jump to the next location where that word is found.

Shortcut: If you hit “/” then “enter”, less will repeat the previous search. less searches from the current location and works its way forward. Note, if you are at the end of the file and search for the sequence “CAA”, less will not find it. You either need to go to the beginning of the file (by typing g) and search again using / or you can use ? to search backwards in the same way you used / previously.

For instance, let’s search forward for the sequence TTTTT in our file. You can see that we go right to that sequence, what it looks like, and where it is in the file. If you continue to type / and hit return, you will move forward to the next instance of this sequence motif. If you instead type ? and hit return, you will search backwards and move up the file to previous examples of this motif.

Remember, the man program actually uses less internally and therefore uses the same commands, so you can search documentation using “/” as well!

There’s another way that we can look at files, and in this case, just look at part of them. This can be particularly useful if we just want to see the beginning or end of the file, or see how it’s formatted.

The commands are head and tail and they let you look at the beginning and end of a file, respectively.

BASH

$  head Streptococcus_agalactiae_18RS21.gbk

OUTPUT

LOCUS       AAJO01000169.1          2501 bp    DNA     linear   UNK
DEFINITION  Streptococcus agalactiae 18RS21
ACCESSION   AAJO01000169.1
KEYWORDS    .
SOURCE      Streptococcus agalactiae 18RS21.
  ORGANISM  Streptococcus agalactiae 18RS21
            Bacteria; Terrabacteria group; Firmicutes; Bacilli;
            Lactobacillales; Streptococcaceae; Streptococcus; Streptococcus
            agalactiae.
FEATURES             Location/Qualifiers

BASH

$ tall Streptococcus_agalactiae_18RS21.gbk

OUTPUT

      241 gcagtatcct gagtacggcg agacacgcga aatctcgtcg gaatctggga ggaccatctc
      301 ccaaccctaa atactctcta gtgaccgata gtgaaccagt accgtgaggg aaaggtgaaa
      361 agcaccccgg gaggggagtg aaatagaacc tgaaaccgtg tgcctacaac aagttcgagc
      421 ccgttaatgg gtgagagcgt gccttttgta gaatgaaccg gcgagttacg atatgatgcg
      481 aggttaagtt gaagagacgg agccgtaggg aaaccgagtc ttaatagggc gtcatagtat
      541 catgttgtag acccgaaacc atgtgaccta cccatgagca ggttgaaggt gaggtaaaac
      601 tcactggagg accgaaccag ggcacgttga aaagtgcttg gatgacttgt gggtagcgga
      661 gaaattcaaa cgaacttgga gatagctggt tctctccgaa atagctttag ggctagcgtc
      721 gatgttaagt ctcttggagt aga
//

The -n option to either of these commands can be used to print the first or last n lines of a file.

BASH

$ head -n 1 Streptococcus_agalactiae_18RS21.gbk

OUTPUT

>LOCUS       AAJO01000169.1          2501 bp    DNA     linear   UNK

BASH

 tail -n 1 Streptococcus_agalactiae_18RS21.gbk

OUTPUT

//

Details on the GBK format

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Although it looks complicated (and it is), it’s easy to understand the fastq format with a little decoding. Some rules about the format include…

Line	Description
1	May start with a “;” or “>”, follows by a name and/or a unique identifier for the sequence, and may also contain additional information
2	The actual DNA sequence
3	If there are more sequences, it always begins with a ‘>’, and info like info in line 1

We can view the first complete read in one of the files our dataset by using head to look at the first four lines.

BASH

$ cd ~/pan_workshop/data/agalactiae_18RS21
$ head -n 10 Streptococcus_agalactiae_18RS21.gbk

OUTPUT

LOCUS       AAJO01000169.1          2501 bp    DNA     linear   UNK
DEFINITION  Streptococcus agalactiae 18RS21
ACCESSION   AAJO01000169.1
KEYWORDS    .
SOURCE      Streptococcus agalactiae 18RS21.
  ORGANISM  Streptococcus agalactiae 18RS21
            Bacteria; Terrabacteria group; Firmicutes; Bacilli;
            Lactobacillales; Streptococcaceae; Streptococcus; Streptococcus
            agalactiae.
FEATURES             Location/Qualifiers

Creating, moving, copying, and removing

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Now we can move around in the file structure, look at files, and search files. But what if we want to copy files or move them around or get rid of them? Most of the time, you can do these sorts of file manipulations without the command line, but there will be some cases (like when you’re working with a remote computer like we are for this lesson) where it will be impossible. You’ll also find that you may be working with hundreds of files and want to do similar manipulations to all of those files. In cases like this, it’s much faster to do these operations at the command line.

Copying Files

When working with computational data, it’s important to keep a safe copy of that data that can’t be accidentally overwritten or deleted. For this lesson, our raw data is our GBK files. We don’t want to accidentally change the original files, so we’ll make a copy of them and change the file permissions so that we can read from, but not write tcdo, the files.

First, let’s make a copy of one of our GBK files using the cp command.

Navigate to the ~/pan_workshop/data/agalactiae_18RS21 directory and enter:

BASH

$ cp Streptococcus_agalactiae_18RS21.gbk Streptococcus_agalactiae_18RS21_copy.gbk

OUTPUT

Streptococcus_agalactiae_18RS21_copy.gbk
Streptococcus_agalactiae_18RS21.fna
Streptococcus_agalactiae_18RS21.gbk

We now, for example, have two copies of the Streptococcus_agalactiae_18RS21.gbk file, one of them named Streptococcus_agalactiae_18RS21_copy.gbk. We’ll move this file to a new directory called backup where we’ll store our backup data files.

Creating Directories

The mkdir command is used to make a directory. Enter mkdir followed by a space, then the directory name you want to create.

BASH

$ mkdir backup

Moving / Renaming

We can now move our backup file to this directory. We can move files around using the command mv.

BASH

$  mv Streptococcus_agalactiae_18RS21_copy.fna backup
$ ls backup

OUTPUT

Streptococcus_agalactiae_18RS21_copy.gbk

The mv command is also how you rename files. Let’s rename this file to make it clear that this is a backup.

BASH

$ cd backup
$ mv Streptococcus_agalactiae_18RS21_copy.gbk Streptococcus_agalactiae_18RS21_backup.gbk
$ ls

OUTPUT

Streptococcus_agalactiae_18RS21_backup.gbk

Removing

When we want to remove a file or a directory we use the rm command. By default, rmwill not delete directories. You can tell rm to delete a directory using the -r (recursive) option.

Let’s delete the backup directory we just made.

BASH

$ cd ..
$ rm -r backup

This will delete not only the directory, but all files within the directory. If you have write-protected files in the directory, you will be asked whether you want to override your permission settings.

If we want to modifiy a file without all the permissions you’ll be asked if you want to override your file permissions. for example:

OUTPUT

rm: remove write-protected regular file 'example.fastq'? 

If you enter n (for no), the file will not be deleted. If you enter y, you will delete the file. This gives us an extra measure of security, as there is one more step between us and deleting our data files.

Important: The rm command permanently removes the file. Be careful with this command. It doesn’t just nicely put the files in the Trash. They’re really gone.

Challenge

Exercise 1(Intermediate): Make backup folder with write-protected permissions

Starting in the /home/dcuser/pan_workshop/data/agalactiae_18RS21 directory, do the following:

1. Make sure that you have deleted your backup directory and all files it contains.
2. Create a copy of each of your GBK files. (Note: You’ll need to do this individually for each of the two FASTQ files. We haven’t learned yet how to do this with a wildcard.)
3. Use a wildcard to move all of your backup files to a new backup directory.
4. Change the permissions on all of your backup files to be write-protected.

Show me the solution

1. rm -r backup
2. cp Streptococcus_agalactiae_18RS21.gbk Streptococcus_agalactiae_18RS21_copy.gbk
3. mkdir backup and mv *_copy.gbk backup
4. chmod -w backup/*-copy.gbk
   It’s always a good idea to check your work with ls -l backup. You should see something like:

OUTPUT

-r-r--r-- 1 dcuser dcuser 4776510 jun  6  2022 Streptococcus_agalactiae_18RS21.gbk

Key Points

• You can view file contents using less, cat, head or tail.
• The commands cp, mv, and mkdir are useful for manipulating existing files and creating new directories.
• You can view file permissions using ls -l and change permissions using chmod.
• The history command and the up arrow on your keyboard can be used to repeat recently used commands.