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 “ghandi.txt” (content below) cat ghandi.txt

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 ghandi.txt
The difference between what we do and what we are capable
of doing

grep -v what ghandi.txt

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 ghandi.txt 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: Pfalciparum.bed and Styphi.fa under practical/Notebooks/files
5. Copy these 2 files under Practical2
6. Check how many lines Pfalciparum.bed contains
7. Display occurrences of the gene PF11_0148 in the bed file
8. Display the names of sequences contained in Styphi.fa (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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