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Unix Commands for Beginners

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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.
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  • BIMM 143 Introduction to UNIX

    BIMM 143 Introduction to UNIX

    BIMM 143 Introduction to UNIX Barry Grant http://thegrantlab.org/bimm143 Do it Yourself! Lets get started… Mac Terminal PC Git Bash SideNote: Terminal vs Shell • Shell: A command-line interface that allows a user to Setting Upinteract with the operating system by typing commands. • Terminal [emulator]: A graphical interface to the shell (i.e. • Mac users: openthe a window Terminal you get when you launch Git Bash/iTerm/etc.). • Windows users: install MobaXterm and then open a terminal Shell prompt Introduction To Barry Grant Introduction To Shell Barry Grant Do it Yourself! Print Working Directory: a.k.a. where the hell am I? This is a comment line pwd This is our first UNIX command :-) Don’t type the “>” bit it is the “shell prompt”! List out the files and directories where you are ls Q. What do you see after each command? Q. Does it make sense if you compare to your Mac: Finder or Windows: File Explorer? On Mac only :( open . Note the [SPACE] is important Download any file to your current directory/folder curl -O https://bioboot.github.io/bggn213_S18/class-material/bggn213_01_unix.zip curl -O https://bioboot.github.io/bggn213_S18/class-material/bggn213_01_unix.zip ls unzip bggn213_01_unix.zip Q. Does what you see at each step make sense if you compare to your Mac: Finder or Windows: File Explorer? Download any file to your current directory/folder curl -O https://bioboot.github.io/bggn213_S18/class-material/bggn213_01_unix.zip List out the files and directories where you are (NB: Use TAB for auto-complete) ls bggn213_01_unix.zip Un-zip your downloaded file unzip bggn213_01_unix.zip curlChange -O https://bioboot.github.io/bggn213_S18/class-material/bggn213_01_unix.zip directory (i.e.