Summary

• Moving around the Filesystem and manipulating files/folders
  • Printing the full path of the current directory pwd
  • Listing files in a directory ls
  • Moving in the file tree cd
  • Making directories mkdir directory_name
  • Copying files cp
  • Moving files mv  - Removing files and directories using rmand rmdir
• Displaying the contents of a file on the screen
  • clear (clear screen) clear
  • Display the content of file using cat
  • Display the content of file using less
  • Display the begin of a file using head
  • Display the end of a file using tail
• Searching the contents of a file
  • Searching word in a file using grep
  • Count for word, line count in a file using wc
• TIPS:
  • Creating and extracting a tar gz archive using tar
  • Compressing and extracting files using gzip
  • Knowing how much space a file or directory is using on a disk with du
  • Creating a file shortcut/ a symbolic link with ln -s  - Downloading a file over HTTP with wget
  • Find files by name or extension
• License

Moving around the Filesystem and manipulating files/folders

Printing the name/full path of the current directory pwd

[tranchant@master0 ~]$ pwd
/home/tranchant

Listing files in a directory ls

ls: list all files in the current directory

[tranchant@master0 ~]$ ls 
AIRAIN
All-EST-coffea.fasta
all-gene.gff3.100000.gene-density
all_no_TE.gff3
all_no_TE.gff3.100000.gene-density
all_no_TE.gff3.10000.gene-density
All-SNP.vcf.density100000.snpden
blast_batch.pl
blast.sh
circos
DEDUP2-1
DEDUP2-all
Desktop
FASTA-TRINITY
fastq-stat.txt
GBS

Listing files in a directory gived as argument ls directory_name

[tranchant@master0 ~]$ ls /home 
abate
abdelrah
adam
adeoti
adereeper
admin
agrondi
aichatou

ls -l : Display the long format listing of all files in the current directory

[tranchant@master0 ~]$ ls -l
total 148272
drwxr-xr-x 10 tranchant ggr      4096 13 mars   2017 AIRAIN
-rwxr-xr-x  1 tranchant ggr  51128305 11 sept. 14:16 All-EST-coffea.fasta
-rw-r--r--  1 tranchant ggr     95117 24 févr.  2017 all-gene.gff3.100000.gene-density
-rwxr-xr-x  1 tranchant ggr  64221458 24 févr.  2017 all_no_TE.gff3
-rw-r--r--  1 tranchant ggr     93796 24 févr.  2017 all_no_TE.gff3.100000.gene-density
-rw-r--r--  1 tranchant ggr    889389 24 févr.  2017 all_no_TE.gff3.10000.gene-density
-rwxr-xr-x  1 tranchant root    90498  5 déc.  07:21 All-SNP.vcf.density100000.snpden
-rwxr-xr-x  1 tranchant ggr     10366 29 mars   2017 blast_batch.pl
-rwxr-xr-x  1 tranchant ggr       878 29 mars   2017 blast.sh
drwxr-xr-x  3 tranchant ggr      4096 19 janv. 15:02 circos
drwxr-sr-x  2 tranchant ggr      4096  8 juin   2017 DEDUP2-1
drwxr-sr-x  2 tranchant ggr      4096  8 juin   2017 DEDUP2-all
drwxr-xr-x  4 root      root     4096  9 juil.  2015 Desktop
drwxr-sr-x  2 tranchant ggr      8192  8 juin   2017 FASTA-TRINITY
-rw-r--r--  1 tranchant ggr      1056 30 nov.  15:31 fastq-stat.txt
drwxr-xr-x  2 tranchant ggr        48 10 août   2016 GBS

ls -a : Display all the files and directories (even hidden files)

[tranchant@master0 ~]$ ls -a
.                                                localConfig.pm
..                                               .localConfig.pm.swp
AIRAIN                                           localConfig-USR.pm
All-EST-coffea.fasta                             LOG
all-gene.gff3.100000.gene-density                .ls_couleur
all_no_TE.gff3                                   .Mathematica
all_no_TE.gff3.100000.gene-density               .matplotlib
all_no_TE.gff3.10000.gene-density                .Megan.def
All-SNP.vcf.density100000.snpden                 Microsatellite_markers
.apollo                                          moduleLoad
.bash_history                                    .mozilla
.bash_logout                                     .oracle_jre_usage
.bash_profile                                    out.sites.pi
.bashrc                                          out.windowed.pi
blast_batch.pl                                   parse-go.pl
blast.sh                                         password.txt
.cache                                           path-new.txt
circos                                           path.sh
.config                                          PATH.sh
.cpan                                            path.txt
Data-TP                                          PERL
.dbus                                            perl5

Moving in the file tree cd

cd DIRECTORY_NAME : change the current working directory to ‘directory’ change directory

[tranchant@master0 ~]$ cd FASTQ

Making directories mkdir directory_name

mkdir directory_name: make a directory in your current working directory type make directory

[tranchant@master0 ~]$ mkdir results

Copying files cp

copy

• cp file1 file2: makes a copy of file1 and calls it file2

• cp file_name directory_name: copy the file file_name to the directory _directory_name’, keeping the same name.

Moving files mv

move

• mv file1 file2 : moves (or renames) file1 to file2. It is used to rename a file, by moving the file to the same directory, but giving it a different name.
• mv file_na me directory : To move the file file_name from one directory to another (here directory_name). This has the effect of moving rather than copying the file, so you end up with only one file rather than two.

Be careful : use preferentially cp command rather than mv command to move big files

Removing files and directories using rmand rmdir

remove

rm file_name: delete (remove) a file (here file_name) To delete (remove) a file, use the rm command. As an example, we are going to create a copy of the science.txt file then delete it.

rmdir directory_name : remove a directory (make sure it is empty first because linux will not let remove a non-empty directory).

Displaying the contents of a file on the screen

clear (clear screen) clear

clear : clears the terminal. Before displaying files, it’s possible to clear the terminal window with this command.

Display the content of file using cat

cat file1 : displays the contents of a file on the screen concatenate

cat file1 file2

cat *.fasta

Display the content of file using less

less file_name : writes the contents of a file onto the screen a page at a time. Less is used in preference to cat for long files.

• Press the [space-bar] if you want to see another page
• Type [q] if you want to quit reading.
• still in less, type a forward slash [/] followed by the word to search

Display the begin of a file using head

head file_name : writes the first ten lines of a file to the screen.

[tranchant@master0 ~]$ head 
head -n 5

Display the end of a file using head

tail file_name : writes the last ten lines of a file to the screen.

[tranchant@master0 ~]$ tail
tail -n 5

Searching the contents of a file

Searching word in a file using grep

grep motif file_name : searches files for specified words or patterns. First clear the screen, then type

To search for a phrase or pattern, you must enclose it in single quotes (the apostrophe symbol). For example to search for spinning top, type

 
# printed out each line containg the word science.

# The grep command is case sensitive; it distinguishes between Science and science.

#To ignore upper/lower case distinctions, use the -i option, i.e. type
[tranchant@master0 ~]$grep -i science science.txt

#
[tranchant@master0 ~]$grep -i 'spinning top' science.txt

Some of the other options of grep are:

-v display those lines that do NOT match -n precede each matching line with the line number -c print only the total count of matched lines

Try some of them and see the different results. Don’t forget, you can use more than one option at a time. For example, the number of lines without the words science or Science is grep -ivc science science.txt

Count for word, line count in a file using wc

wc: short for word count (word count)

Creating and extracting a tar gz archive using tar

• To create a tar.gz archive from a given folder

 
# compress the contents of source-folder-name to a tar.gz archive named tar-archive-name.tar.gz
[tranchant@master0 ~]$tar -zcvf tar-archive-name.tar.gz source-folder-name 

• To extract a tar.gz compressed archive

 
# extract the archive to the folder tar-archive-name. 
tar -zxvf tar-archive-name.tar.gz 

Compressing and extracting files using gzip

• gzip {filename}
• gzip -d {.gz file}

Knowing how much space a file or directory is using on a disk with du

du [options] [file or dir]

If you use it with no arguments you will the usage of all files and directories (recursively) of the working directory.

-h : Shows the in human readable format -s : Sumarize, so it displays the total of each subdirectory and not for its contents

Creating a file shortcut/ a symbolic link with ln -s

A symbolic link, also termed a soft link, is a special kind of file that points to another file, much like a shortcut in Windows or a Macintosh alias.

ln -s source_file myfile

• source_file corresponds to the name of the existing file for which the symbolic link is created (this file can be any existing file or directory across the file systems).
• myfile is the name of the symbolic link.

Note :

• If the source file is deleted or moved it to a different location, the symbolic file will not function properly and should be either deleted or moved it.

Downloading a file over HTTP with wget

wget http://website.com/files/file.zip : downloads the file http://website.com/files/file.zip into the working directory.

Find files by name or extension with find

find options path motif_file

• the path argument defines the top level directory where find begins filtering
• the motif_file argument gives the motif searched in the filename within the directory (and all sub-directories)

The following example search for k64 files in the current directory and all sub-directories:

[durreuic@cobalt172 ~]$find . -name "*k64*" 
./mappingGlabv2/fastqPairedUnmappedBartiivsOmap/TEST/k64ctg-TOGGLEmappingRE
./mappingGlabv2/fastqPairedUnmappedBartiivsOmap/TEST/k64`

License

The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).