Unix commands for beginners D. Puthier TAGC/Inserm, U1090, [email protected] Matthieu Defrance, ULB, [email protected] Stéphanie Le gras, Igbmc, [email protected] Christophe Blanchet, IFB, [email protected] MATE Desktop Demo Quick overview. Installation: http://www.france-bioinformatique.fr/?q=fr/core/cellule-infrastructure/documentation-cloud Dashboard: https://cloud.france-bioinformatique.fr/cloud/instance/ The terminal… Demo Type ‘ls’ in the terminal (list files) # list files root@vm: ls How can I speak to the terminal ● Answer : you can speak in BASH (Bourne Again Shell) * ○ BASH is one of numerous shell dialect (ksh, csh, zsh,...). ○ All this shell languages are extremely similar. ○ These languages are based on commands. ○ These modular commands allows one to perform tasks. * Reférence (calembour) au premier langage Shell écrit par Stephen Bourne :) Command prototype(s) (1) ● One command performs a task (sort, select, open, align reads,...). ● A command has arguments that may be facultative and modify the way it works. ● These arguments may take some values. ● Most of the time an instruction (command line) starts with a command name (or path to the command). ● In the example below we will say minus v’. # Argument without any associated value # depending on the command v means verbose, version (or other) fastqc -v # An argument with an associated value man -k jpeg Command prototype(s) (1) ● Most of the time arguments can be written in their short of long form (more explicit/better readability). ● Long form are generally precede with ‘--’ (for instance ‘minus minus apropos’) # Long form without any associated value. fastqc --version # Long form with an associated value. man --apropos jpeg Getting help ! Call you friends or better use man (manuel) # Demo root@vm: man ls # getting help about ls root@vm: man man # getting help about man ... Help shortcuts: /foo : search for ‘foo’. n : (next) next occurence of ‘foo’. p: (previous) previous occurrence of ‘foo’. q : quit help page. Our first command: ls The ls command and some of its arguments ● ls can take several arguments. ● Main arguments: ○ -l : (long) get lot of information. ○ -a (all) show all files including hidden files*. ○ -1 : show results as 1 column. ○ -t (time) sort results by date/time. ○ -r (reverse) reverse sort order. ● One can combine arguments ○ ls -l -a ○ ls -la * Under linux hidden files start with a ‘.’ (e.g ‘.thehiddenfile.txt’). The ls command and some of its arguments # Demo root@vm: ls # list files root@vm: ls -a # list files including hidden files * root@vm: ls -l # get lot of information about files root@vm: ls -1 # list file (one column) root@vm: ls -t # List file by modification date ** # Combining arguments root@vm: ls -rtl # lot of info, sort by date, reverse order * WARNING with spaces. Instruction should start with a command. The ls-a command does not exists ! ** Default sorting is case-sensitive sorting. Create directories and files File system tree ● The file system can be viewed as a tree in which nodes are directories or files. ● This tree has a root: / ● The root folder (/) contains ○ A root folder an various additional folder* ■ Under IFB machine your root folder contains a Documents folder * Under IFB VM, you are the root/sysadmin, this is a particular case. Hos should I refer to a file/directory ● 1) By specifying the path from the root. Absolute path. e.g; /root/Documents /root/Music ● 2) By referring to the current location/directory (the working/current directory). Relative path. Syntax for relative path # The upper directory relative to the working directory .. # Two directories up ../.. # Three ../../.. # The current working directory ./ File system: Demo pwd (print working directory); cd (change directory). * root@vm: pwd # The current working directory (/root) root@vm: cd /root/Documents # We go into Documents root@vm: pwd # /root/Documents root@vm: cd .. # go up one level (/root) root@vm: cd /root/Music # Go to the Music folder root@vm: pwd # /root/Music root@vm: cd ../.. # Go to the root of the file system root@vm: ls # You should see the root directory root@vm: cd /root/Music # Let’s go to the root/Music directory root@vm: cd ../Documents # And to the Document folder * Use complétion (tab key) for file, directories and commands. File system: some hints ● If you are the /root your data are stored in /root ○ i.e ‘user directory’ or home. ● ~ (tilda) contains the path to your home (same as $HOME). root@vm: cd / # At the root root@vm: pwd # / root@vm: cd ~/Documents # The Document directory of your home folder. root@vm: cd ~ # go to your home dir. root@vm: cd /usr/local/bin # Go to /usr/local/bin root@vm: ls ~ # list files in your ‘home’ directory root@vm: cd ~/Music # Go to the Music folder inside your home dir. root@vm: cd # == cd ~ Make directories ● We will use the mkdir (make directory) command. root@vm: mkdir projet_roscoff # Create a directory root@vm: cd ./projet_roscoff # == cd projet_roscoff * root@vm: mkdir rna-seq # Let’s create a folder root@vm: mkdir chip-seq dna-seq # and several sub-folders root@vm: ls -1 # list files and folders root@vm: cd chip-seq # == ./chip-seq root@vm: pwd # the current working dir root@vm: cd ../.. # go back home * ./ is most of the time facultative Hands on ● 1) go to ~/projet_roscoff/chip-seq ● 2) From this directory create a directory named annotation in ~/projet_roscoff/ ● Go inside annotation directory ● Check you are in the write place ● Go back home. Hands on ● 1) go to ~/projet_roscoff/chip-seq ● 2) From this directory create a directory named annotation in ~/projet_roscoff/ ● Go inside annotation directory ● Check you are in the write place ● Go back home. ● # Solution root@vm: cd ~/projet_roscoff/chip-seq root@vm: mkdir ../annotations root@vm: cd ../annotations root@vm: cd Manipulate files Download and uncompress files ● We will use the wget command to download files. ● To uncompress we will use gunzip if the file was compressed with the gzip algorithm (extension .gz) root@vm: cd ~/projet_roscoff/annotations # on se déplace dans annotations # On télécharge le fichier root@vm: wget http://pedagogix-tagc.univ-mrs.fr/courses/data/roscoff/hg19_exons.bed.gz root@vm: ls # le fichier compressé root@vm: ls # le fichier compressé root@vm: gunzip hg19_exons.bed # on le décompresse root@vm: ls # le fichier a perdu l’extension gz The hg19_exons.bed file Contains coordinates (start/end) of humand exons in bed format. Bed format (Bed6) ( http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ) * Tabulated format (how to check that ???) Chromosome Start End Name Score Strand (Others…) * Start and End position are always given relative to the 5’/3’ orientation of the + strand. Coordinates are ‘zero-based, half-open’. Visualising file content ● With a pager: less or more (do more or less the same). ● With head ou tail to display the n first or n last lines of a file. ● The cat command allows to send file content to the screen. <ctrl> + c to cancel. ● The shortcuts for less are the same as for the man command. Raccourcis dans less: ↑ : go up. ↓ : go down. > : go to first line. < : go to last line. /foo : search for ‘foo’. n : next occurrence of foo. p: previous occurrence of foo q : quit. Hands on ● 1) Look at the ten first lines of hg19_exons.bed with head. ● 2) look at the ten last lines of hg19_exons.bed with tail. ● 3) Go through the hg19_exons.bed file with less. ● 4)Send file content to the screen with cat. Exercices ● 1) Look at the ten first lines of hg19_exons.bed with head. ● 2) look at the ten last lines of hg19_exons.bed with tail. ● 3) Go through the hg19_exons.bed file with less. ● 4)Send file content to the screen with cat. # Solution root@vm: head -n 10 hg19_exons.bed root@vm: tail -n 10 hg19_exons.bed root@vm: less hg19_exons.bed root@vm: cat hg19_exons.bed Counting line number This can be done with the wc (word count) command with -l (line) argument. root@vm: wc -l hg19_exons.bed # 484127 exons Extract columns ● Use the cut command with the -f (field) argument ● The columns must be tabulated or use the -d argument (‘delimiter’) root@vm: cut -f1 hg19_exons.bed # Column 1 root@vm: cut -f1,2 hg19_exons.bed # Columns 1 and 2 root@vm: cut -f3-5 hg19_exons.bed # Columns from 3 to 5 root@vm: cut -f3- hg19_exons.bed # Column 3 to the last column Sort a file ● On should use the sort command (alphabetic sorting by default). ○ -k (key): e.g ■ -k1,1: sort by column 1. ■ -k2,2nr: sort by column 2 using a numeric sorting in reverse order. ■ -k2,2g: sort by column 2 (decimal sorting). Example: sort hg19_exons.bed by chromosomes then by genomic coordinates: root@vm: sort -k1,1 -k2,2nr hg19_exons.bed Redirections Command pipes Input Output Input Output Input Output Commande Commande Commande Error Error Error ● Standard Input: a file or text stream. ● Standard output: screen by default. ● Standard error: may be capture for log purpose. Demo: command pipes Obtenir la liste de chromosomes présents dans le fichier root@vm: cut -f1 hg19_exons.bed | sort | uniq # La liste non-redondante des chromosomes Obtenir la liste des chromosomes présents dans le fichier et leur nombre root@vm: sort hg19_exons.bed | uniq -c # -c pour ‘count’ Compter le nombre de transcript non codant (contenant ‘NR_’). root@vm: cut -f4 hg19_exons.bed | grep "NR_" | sort | uniq | wc -l #11675 Note: La commande uniq permet d’éliminer les doublons dans un fichier trié. Note: la commande grep permet de chercher une chaîne de caractères. Exercices (notés) ● How many exons on chromosome 22 ? ● What is the most frequent chrom-start-end tuple ? ○ i.e The most frequent exon.