Introduc)on to Unix and Perl programming

Transcription

1 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Department of Systems Biology Technical University of Denmark Introduc)on to Unix and Perl programming EDITA KAROSIENE PhD student April 18, 2012

2 Introduc)on I learned Perl 5 years ago and since then was using it almost daily in my research The course at CBS: Perl and Unix for Bioinforma0cians hgp:// The teacher: Peter Wad Sacke7 Computer scienlst System administrator Teaching Perl for 10 years The best learning is by doing

3 Introduc)on to UNIX UNIX is a mull- user, mull- tasking operalng system for servers, desktops and laptops UNIX- like operalng systems: Sun Solaris GNU/Linux MacOS X The shell: Acts as an interface for the user Is a command line interpreter (CLI) Processes and files: A process is an execulng program idenlfied by a unique process idenlfier A file is a colleclon of data. Files are created by users using text editors, running programs etc.

4 Introduc)on to UNIX Write your commands in the shell

5 Introduc)on to UNIX Create and edit files using text editors: nedit emacs Xemacs vi vim We are going to use nedit for the course

6 Main UNIX commands When you open the shell, your current working directory is your home directory List the content of a current working directory: ls List in a long format: ls - l Make a new directory: mkdir newdir Change current working directory to a new directory: cd newdir cd.. cd../.. cd /home/people/edita/perl cd when the directory newdir is in the current directory go one directory up the hierarchy go two directories up the hierarchy specify full path to the directory go to home directory

7 Main UNIX commands Print working directory find out where you are: pwd ( ~ ) refers to your home directory: ls ~ cd ~/newdir list the content of your home directory goes to newdir from whenever you are (. ) refers to your current directory

8 Main UNIX commands Copy one file to another: cp myfile mynewfile Copy a file to a directory: cp myfile newdir/ Copy a file to the current working directory: cp ~/newdir/myfile. Move (or rename) files: mv myfile mynewfile gives a new name to the file mv myfile newdir/ moves the file from one directory to another

9 Main UNIX commands Remove (delete) a file: rm myfile Remove (delete) a directory: rmdir newdir/ if the directory is empty rm - r newdir/ recursively remove directory with all its content Display the content of files: cat myfile all at once less myfile a page at a 7me head myfile shows the first 10 lines head n 50 myfile shows the first 50 lines tail myfile shows the last 10 lines

10 Main UNIX commands Search for pagerns, words in a file: grep keyword myfile displays the lines that contain keyword Count lines, words, characters in the file wc myfile gives number of lines, words and characters wc l myfile gives number of lines in the file

11 Main UNIX commands Redirec)ng Processes in UNIX: write to standard output terminal screen take input from standard input keyboard Redirect the output of the command to the file: cat myfile > newfile grep keyword myfile > newfile Append to the file: cat myfile >> newfile Pipe the output of one command as the input for another command: grep keyword myfile wc - l

12 Now it s your turn! SOLVE EXERCISE 1

13 Time for a break! B r e a k!

14 Introduc)on to Perl Perl is a high- level, general- purpose, interpreted, dynamic programming language Strengths of Perl: It is easy to learn, and learning a ligle helps to achieve a lot It is very portable available for a huge variety of operalng systems It has very powerful text parsing facililes The syntax language is quite as a human language Quick development Weaknesses of Perl: No as quick as compiled languages Easy to make messy, ugly and hard to maintain code

15 Perl sources Books: Learning Perl, 4th ed. by Randal Schwartz & Tom ChrisLansen (O'Reilly) Programming Perl, 3rd ed. by Larry Wall, Tom ChrisLansen & Jon Orwant (O'Reilly) Links: hgp:// hgp://perldoc.perl.org/ hgp://cpan.perl.org/ hgp:// perl/ Main Perl web site Perl documenta7on Perl module/library repository Online Perl book

16 First steps in Perl We write Perl programs using text editor (e.g. nedit) Perl programs in UNIX have an extension.pl nedit myprogram.pl Each Perl program starts with a line: #! /usr/bin/perl - w Ager we finish the program, we should save it and make it executable: chmod 755 myprogram.pl We run our Perl program like this: perl myprogram.pl./myprogram.pl Each line in Perl program ends with ; For comments in the code use #

17 Variables Variables store values of data All variables (scalars) starts with $ A variable name may contain alphanumeric characters and underscore A simple variable can be: a string floalng point number does not need to be declared as any specific type Examples: $var1 $i $MyCount $remember_this

18 Assigning values to variables Numbers are assigned in a natural manner: $num = 1; $num = ; $num = ; Strings are assigned with quotes: $string = This is a literal string ; $string = This is an $interpolated string\n ; Interpolated strings are searched for variables and special character combinalons Special character combinalons that have meaning: \n for new line \t for tab If a number is used in a string context then it is changed to a string and vice versa

19 Operators Operators take arguments, do something with them and return a value Numeric operators: ArithmeLc operators: +, -, *, /, **, % Bitwise operators: (or), & (and), ^ (xor), ~ (not) String operators: ConcatenaLon combine strings together string1. string2 RepeLLon repeats a string a given number of Lmes string1 x3

20 Prin)ng output print statement prints a comma separated list of values: print Hello world\n ; print Result is, $num1 + $num2, \n ; print My name is $name\n ; The output of print goes to the last selected filehandle unless otherwise specified. This is usually STDOUT, which is usually the screen.

21 SOLVE EXERCISES 2-4 Edita Karosiene

22 B r e a k!

23 Condi)onal statement A standard if statement: if (condi0onal_statement) { # this will be executed if the statement is true } if statements exists in various forms in perl: if (condi0onal_statement1) { # this will be executed if the statement is true } elsif (condi0onal_statement2) { # this will be executed if this statement is true } else { # finally this is excuted if no statements were true }

24 Condi)onal statements Condi0onal statements may involve logical operators and usually test equality or compare one value to another Numerical comparison operators: < > <= >= ==!= <=> String comparison operators: lt gt le ge eq ne cmp Boolean operators: && (and) (or)! (not) xor Examples: $age > 18 and $height < 1.4 ($name eq Peter or $name eq John ) and $wage <= 25000

25 Condi)onal statements CondiLonal statements can be turned around: unless (condi0onal_statement) { # this will be executed if the statement is false } Example with condilonsl statements: if ($x == 7) { print The number is 7 ; } elsif ($x == 8) { print The number is 8 ; } else { print The number is not 7 and not 8 ; }

26 Loops - while while loops conlnually iterate as long as the condilonal statement remains true The standard while loop: # some ini)aliza)on while (condi0onal_statement) { # code which is executed while the statement is true # change the ini)alized value } Example: $count = 0; while ($count <= 7) { print "$count\n"; $count++; } Note: $count++ $count = $count + 1

27 Loops - for The for loop allows you to define the following steps in one easy line of code: Set a counter variable to some inilal value Check to see if the condi0onal statement is true Execute the code within the loop Increment a counter at the end of each iteralon through the loop Each step is separated by a semicolon: for ( ini)alize a counter; condi)onal statement; increment a counter) { do this code; } Example: for ($count = 0; $count <= 7; $count++) { print "$count\n"; }

28 Ge}ng input from STDIN Usually STDIN is the keyboard unless redireclon is in play Lines are read from the keyboard like this: $line = <STDIN>; When reading a line, it is important to realize that a line ends with a newline, which is part of what is read. You have to get rid of that newline: chomp $line; To ask user for the input just use print statement: print Please enter your name\n ; $name = <STDIN>; Exmaple of the simple Perl program

29 SOLVE EXERCISES 5-9

30

31 The defined func)on Variables have the special undef value before they are assigned undef automalcally acts like 0 when used as a number and as an empty string in a string context To check if the variable is defined use defined funclon: if (defined $var) {} The funclon is ogen used to check if there is no more input the end of the file will return undef: $line = <STDIN>; if (defined ($line)) { print $line\n ; } else { print No input\n ; }

32 Redirec)on When input is given from the keyboard, Ctrl+d corresponds to the end of the file When redireclon is used, the input is taken from the file:./my_program.pl < input_file.txt this is wrieen in the shell as a command The program will take one line at a Lme from the file unll the end of the file Another way: cat input_file.txt./my_program.pl Be careful not to do this: cat input_file.txt >./my_program.pl The output of the program can also be redirected to a file:./my_program.pl > output_file.txt Also, the program can take file as an input and write the output to another file:./my_program.pl < input_file.txt > output_file.txt

33 SOLVE EXERCISES 10-11

34 B r e a k!

35 Filehandles Very ogen you want your program to read from or write to a file For this we need filehandles Filehandle is a label which gives us a handle on the file we want to work with <STDIN> is a filehandle for the special file called standard input Afilehandle for standard output is STDOUT and can be used like this: print STDOUT Hello world\n ; Filehandles are named like other Perl idenlfiers (using legers, digits and underscores) but can not start with a digit

36 Opening and closing files The modern open is a three parameters funclon call: open(filehandle, $mode, $filename) The usual file modes are: < reading > wrilng >> appending +< reading and wrilng Examples: open (IN, <, input_file.txt ); open (OUT, >, output_file.txt); open (OUT, >>, $filename); open file for reading open file for wri7ng open file for appending The files are closed only using filehandle: close IN;

37 Reading files Ager opening the file, you can read it line- by- line using a filehandle Two common ways to read a file line- by- line: 1. open(in, '<', $filename) or die "Can't read file\n"; $line = <IN>; while (defined $line) { print $line; $line = <IN>; } close IN; 2. open(in, "<", "ex1.acc") or die "Can't read file\n"; while (defined ($line = <IN>)) { print $line; } close IN;

38 SOLVE EXERCISES 12-14

39 Round up for today You learned the basics of UNIX, so you can make simple operalons in UNIX- like environments Use man to learn more about each command You learned basics of Perl so that you can write simple programs to handle your problems If you are slll not too comfortable do not worry it takes Lme to understand how this really works Don t worry if the program is not working and you can not find the mistake! Even experienced users can struggle for hours trying to find an error which turns out to be a missing semicolon If you can not think about the solulon immediately, leave it for a while it might come to your head when you least expect! The best learning is by doing!

40 Thank you for today!