Part II: reading files, extracting

information from files and files

permissions

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 Text editors

• nano: a simple and easy-to-use text editor

• Is installed by default in many other Linux
distributions
• gedit is also very easy to use
• vim, emacs, Geany: excellent programs but do
require some learning
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 Get started with
name of the program
name of the program and version number,
and version number,

nano

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Get started with nano
• nano file1
• Type “my first test file with nano”
• Hit enter to move to another line and type “the second
line of test”
• One you finish typing, hit Ctrl+x
• Save modified buffer (ANSWERING "No" WILL
DESTROY CHANGES) ?
• Hit Y
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Basic manupulating file commands

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Displaying whole content of a file or parts of it (default + options)

• cat: view the content of a short file cat

<filename>
• more: view the content of a long file and navigate through it more
<filename>
• less: view the content of a long file, by portions less
<filename>
• head: view the first lines of a long file
head <filename>
• tail: view the last lines of a long file tail
<filename>

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View file content: less command

• less command displays a text file content, one

page at a time
• Structure: less filename
• Move a page down: either use the page down key
or space
• To exit less, type q
• To go to the end of the text file, type g
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 Head and tail commands

• head command displays a text file content, by default: 10 first lines

at a time
head <options> <filename>

• tail command displays a text file content, by default: 10 last lines at

a time
tail <options> <filename>

use –n to change the number of lines you want to display

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 Basic manupulating file commands

Copy, move and remove

• cp: copy files and directories cp <pathfrom>
<path to>
• mv: move or rename files and directories mv <pathfrom>
<path to>
• rm: remove files and directories
rm pathname
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 Copying command: cp

• Simplest form: cp file1 file2

🡺 Copy the contents of file1 into file2. If file2 does not exist,
it is created. Otherwise, file2 is silently overwritten with the
contents of file1.

• cp filename dirpath
🡺 Make a copy of the file (or directory) into the specified
destination directory

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Copying command: mv
The mv command moves or renames files and directories depending on how it is used
• To rename a file:
mv filename1 filename2
If file2 exists, its contents are silently replaced with the contents of file1. To avoid
overwriting, use the interactive mode:
mv -i filename1 filename2

• To move a file (or a directory) to another directory:

mv file dirpath
• To move different files (or a directory) to another directory:
mv file1 file2 file3 dirpath
• To move directory to another directory:
mv dir1 dir2
If dir2 does not exist, then dir1 is renamed dir2. If dir2 exists, the directory dir1 is moved within
directory dir2

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The rm command
The rm command deletes files and directories

To remove a file:
rm filename
To remove many files:
rm filename1 filename2

Add the interactive mode to prompt user before deleting with –i

rm -i filename1 filename2

Delete directories with all their contents

rm -r dir1 dir2
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 Be careful with rm !

• Linux does not have an undelete command

• Once you delete something with rm, it's gone!
• You can inflict terrific damage on your system with rm
if you are not careful, particularly with wildcards
• Try this trick before using rm: construct your
command using ls instead first

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Some statistics about your file content: wc command

• wc prints newline, word, and byte counts for each file

wc <options> <filename>

Some useful options:

• -c: print the byte counts
• -m: print the character counts
• -l: print the newline counts
• For more info about the different commands, remember to use
man commandname
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Extracting data from files

• grep: to search for the occurrence of a specific pattern

(regular expression using the wildcards…) in a file
grep <pattern> <filename>

• cut: is used to extract specific fields from a file cut

<options> <filename>

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grep command

• grep (“global regular expression profile”) is used to search for the

occurrence of a specific pattern (regular expression…) in a file
• grep outputs the whole line containing that pattern

Example:
Extract lines containing the term sequence from a file: grep
sequence <filename>
Extract lines that do not contain pattern xxx from a file: grep
–v sequence <filename>

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 grep example

Let’s create a file named “[Link]” (content below) cat [Link]

The difference between what we do and what we are capable of
doing would suffice to solve
most of the world's problems
grep what [Link]
The difference between what we do and what we are capable
of doing

grep -v what [Link]

would suffice to solve
most of the world's problems

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cut command

• cut is used to extract specific fields from a file cut

<options> <filename>
• For <options> see man
• Important options are
• -d (field delimiter)
• -f (field specifier)
Example:
extract fields 2 and 3 from a file having ‘space’ as a separator cut -d’ ‘ -f2,3
<filename>

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Practical 2

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Instructions

1. Create the file [Link] under Practical2

2. Display lines that contain “what” and those that don’t
3. Count how many words are there in that file
4. Now, we will use 2 files: [Link] and [Link] under practical/Notebooks/files
5. Copy these 2 files under Practical2
6. Check how many lines [Link] contains
7. Display occurrences of the gene PF11_0148 in the bed file
8. Display the names of sequences contained in [Link] (in a fasta file, each sequence
is preceded by a description line starting with > and containing the sequence
name/ids often followed by additional info)

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Additional details about cp and nano

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 Some nano shortcuts
• To search for a text string, hit Ctrl+W, and enter your search term
• This search can then be cancelled mid-execution by hitting Ctrl+C
without destroying your buffer
• Ctrl+X: finish typing and close an open file

Remember: nano

- Opens the file if it’s already existing, you can modify and save
changes
- Creates a new file in the specified path if it does not exist
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 Other examples: cp

• Add the interactive mode with the option -i

• cp -i file1 file2
🡺Same as the previous one. However, if file2 exists, the user is
notified before overwriting file2 with the content of file1
• cp –R pathdir1 pathdir2
🡺 Copy the contents of the directory dir1. If directory dir2 does
not exist, it is created. Otherwise, it creates a directory named
dir1 within directory dir2

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