SRM UNIVERSITY DEPARTMENT OF BIOINFORMATICS

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1 LIST OF EXPERIMENTS 1. Basic UNIX Commands 2. Working with vi editor 3. Working with emacs editors 4. Advanced UNIX Utilities 5. Creating a Bioinformatics directory 6. Simple Perl Program (Operators) 7. Use of <STDIN> 8. Chop and Chomp Operators 9. Control Structures: a) If If else statements b) While statement c) foreach and Until Loops 10. Subroutines, Subroutines using array and special variables 11. Random Number Generation 12. Simple programs using File Functions 13. Hash Traversal Functions 14. Command Line Arguments 15. Setuid / setgid Perl Scripts 16. Creating a static HTML file by a Perl Program 1

2 EX.NO: 1 DATE: BASIC UNIX COMMANDS AIM: To execute all the basic commands in UNIX PROCEDURE: Open Terminal and execute all the following Basic UNIX commands: Command name : mkdir Descripti on : Creating a directory Options Example : Nil : >mkdir directory name O utput : /home/username/directoryname Command name : cd Description : change directory Options : cd.. move one level down cd/ to go to the root directory cd~ to go to the home directory cd../.. move two levels up Example : >cd directory O utput : /home/username/directory Command name Description Options Example Output : ls : listing contents of the directory : ls l listing the contents of the file in list fashion ls lc listing the contents of the file in column of fashion ls t listing the contents of directory according to time ls x listing the contents of directory in rows ls m listing the contents of directory separated by commas ls R recursively displaying the files and directories : >ls sequences : analysis assembly 2

3 Command name Description Example O ptions Command name Descripti on Options Exampl e O utput : mv : moving or renaming a file or a directory : mv*.seq/user.sequences all files with.seq extensions are moved to user directory mv i94h10.seq ignores the case mv94{h,h}10.seq it is used to rename the file : >mvac txt94h10.seq : 94H10.seq : cp : copying a file : Nil : >cp Ac(4H10.seq{,.bak} : Adds extension.bak to all sequence files Command name : head and tail Descriptio n : used to display top few or bottom few lines of a line Options : Nil Example : >head 94H10.seq >tail 94H10.seq Output : It displays the first and last ten lines of 94H10.seq Command name : cat Descripti on : create, view and append or change the contents of a file Options : Nil Example : cat>new Output : a new file is created Command name : rm and rmdir Descripti on : removing a file or a directory Options : nil Example Output : rm r seq x : removes all files starting with seq(recursive deletion) 3

4 Command name : find Descript ion : searching a particular file or a directory Options : nil Example : find. name seqchr* O utput : finds all the files starting with seqchr* as a part of it Command name : more Descript ion : displays the contents of the file Options : nil Example : more 94H10.seq Output : prints contents of the file 94H10.seq Command name : chmod Descrip tion : used to change the permissions of a file Options : nil Example : chmod 777 file.txt O utput : gives read, write and execute permissions to user, group and world Command name : ps Descriptio n : process tracking (to find how many processes are running) Options : nil Example : >ps Output : PID TTY TIME COMMAND Command name : kill Description : used to stop the process Options : nil Exampl e : >file.txt O utput : it the stops the processes of file.txt Command name Description : tar : related files are grouped together 4

5 NAME : Bhupendra Khandelwal REG NO : Options : tar cvffile1.tar tar tvf tar xvf tar cvf Example : tar cvf*.seq Output : archive seq files in the current directory MISCELLANEOUS COMMANDS: Command name : gzip/compress and gunzip/uncompress Description : gzip file is compressed to size smaller than compress. Compress used to compress file but size greater than that obtained by gzip. Uncompress used to uncompress file but size smaller than that obtained by gunzip. Options : nil Example : >gzip test. tar >compress test.tar Output : test.tar.gz Test.tar.z RESULT: The Basic UNIX Commands were thus executed and the output as noted. 5

6 EX.NO: 2 DATE: AIM: To study the various UNIX commands Vi EDITOR COMMANDS PROCEDURE: Open Terminal and open vi editor. Try out the following commands: Sav ing and Quitting: :q quit without saving :q! quit without saving even changes are made :w save and continue editing :wq save and quit :zz write file only if changes were made and quit :x same function as zz Moving around text: h move cursor one character left i move cursor one character right k move cursor up one line j move cursor down one line G move to end of file H move to top line visible on screen L move to last line visible on screen M move to middle line visible on screen w move forward word by word b move backward word by word W move forward one word ignoring punctuation e move end of word O move to beginning of line $ move to end of file 6

7 NA ME : Bhupendra Khandelwal REG NO : Changing, Deleting, and Substituting text cc change a single line C change text from cursor to end of line x delete cw change a single word, single character under cursor X delete single character before cursor dw delete a word d{ } delete upto next paragraph dd delete current line D delete from cursor to end of line dl delete upto last line of screen dg delete to end of line j join two lines rx replace one character with x R override characters s substitute a character S substitute a line u undo last change U restore current line Scrollin g and Indenting Text: <ctrl>f scroll forward one window <ctrl>b scroll back one window > > shift current line forward one indent width < < shift current line back one indent width Finding and Searching for text: fx find first occurrence of character x ahead of cursor Fx find first occurrence of x behind cursor Cutting and Pasting: Y copy correct manual p put deleted text after or below cursor P put deleted text before or after cursor RESULT: The vi editor commands were successfully executed and the output was noted. 7

8 EX.NO: 3 DATE: EMACS EDITOR COMMANDS AIM: To study the various commands in emacs editor PROCEDURE: 1. Open Terminal and create an emacs file using the command, #emacs <filename> 2. Insert text using the emacs editor 3. Perform the following operations using the various emacs editor commands and note the output ESSENTIAL EMACS COMMANDS: Ctrl + A: Move to the beginning of the line Ctrl + E: Move to the end of the line Ctrl + S: Start search text Ctrl + d: Delete single character in a line Ctrl + K: Delete entire line upto cursor Delete: Delete character before cursor Ctrl + _: Undo last action Ctrl + X/ Ctrl + S: Save current file and exit Ctrl + X/ Ctrl + C: Exit emacs without saving Home: Go to the beginning of the document End: Go to the end of the document 8

9 MISCELLANEOUS EMACS COMMANDS: Ctrl + P: Move to the previous line Ctrl + N: Move to the next line Ctrl + F: Move forward one character Ctrl + B: Move backwards one character Ctrl + V: Scroll down one page Esc V: Scroll up one page Esc F: Move ahead word by word Esc B: Move backward word by word Esc A: Move to the beginning of the sentence Esc E: Move to the end of the sentence The commands were executed on emacs editor and changes were observed. RESULT: The basic emacs editor commands were successfully executed and the output was noted. 9

10 EX.NO: 4 DATE: ADVANCED UNIX UTILITIES AIM: To study the syntax and usage of various UNIX utilities such as grep and uniq. PROCEDURE: Open Terminal and perform the advanced commands (Utilities) described below: 1. grep Utility name : grep Description : global search for regular expressions Options : searches given keywords and prints files containing it Example : >grep v ase genes.txt! more Output : all lines that do not carry the string ase are printed out with the v option 2. wc Utility name : wc Description : gives number of lines, words and characters in a file Options : wc 1 gives number of lines wc w gives the number of words wc c gives the number of characters Example : >wc mydetails.txt Output : uniq Utility name : uniq Description : deletes the repeted text in a file Options : uniq c gives the text along with the number of times they are present Example : >uniq test.txt 10

11 Output : This Is Some Repeated Text 4. sort Utility name: Description : used for sorting the contents of a file Options : sort r to sort in descending sort f ignores case separator sort t ignores files separator sort M orders based on month Example : >sort test.txt Output : Is Some Repeated Text This 5. awk Utility n ame : awk Description : helps to print contents of file based on given conditions Options : nil Example : >cat>test.txt 1 one a 2 two b 3 three c >awk {print $1} test.txt 11

12 Output : RESULT: The advanced UNIX Utility commands were successfully executed. 12

13 EX.NO: 5 DATE: CREATING A BIOINFORMATICS DIRECTORY AIM: To create a Bioinformatics Directory Structure to study the basic UNIX commands. Structure: Root Home Sequences Assembly Analysis Human Mouse Rice Human Mouse Rice Ch22 Chr22 Chr5 Chr22 Chr22 Chr5 Chr10 Chr10 Chr4 Chr10 Chr10 Chr4 Chr5 Chr5 13 Chr5 Chr5

14 PROCEDURE : COMMANDS: 1. Open terminal (Shell) 2. Create a Bioinformatics Directory using the following commands to make files and folders in the main directory $ mkdir sequences $ cd sequences $ mkdir assembly $ cd assembly $ mkdir human $ mkdir mouse $ mkdir rice $ cd human $ mkdir chr22 $ cd chr22 $ mkdir chr10 $ cd chr10 $ mkdir chr5 $ cd chr5 $ cd.. $ cd.. $ cd.. $ cd mouse $ mkdir chr22 $ cd chr22 $ mkdir chr10 $ cd chr10 $ mkdir chr5 $ cd chr5 $ cd..\.. $ cd.. $ cd rice $ mkdir chr5 14

15 $ cd chr5 $ mkdir chr4 $ cd..\.. $ cd.. $ cd analysis $ mkdir human $ mkdir mouse $ mkdir rice $ cd human $ mkdir chr22 $ cd chr22 $ mkdir chr10 $ mkdir chr5 $ cd chr5 $ cd.. $ cd.. $ cd.. $ cd mouse $ mkdir chr22 $ cd chr22 $ mkdir chr10 $ cd chr10 $ mkdir chr5 $ cd chr5 $ cd..\.. $ cd.. $ cd rice $ mkdir chr5 $ cd chr5 $ mkdir chr4 $ cd~ RESULT: The Bioinformatics directory was successfully created using various UNIX Commands. 15

16 EX.NO: 6 DATE: SIMPLE PERL PROGRAM AIM: To illustrate the basic structure of Perl program. PROCEDURE: PROGRAM: 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output $aminoacid="methionine"; $protein="lysin"; print "aminoacid=$aminoacid\n"; print"protein= $protein\n"; $msg="welcome to perl programming for bioinformatics"; print "$msg\n"; RESULT: A simple perl program using print function was successfully executed 16

17 SIMPLE SCALAR PROGRAM AIM: To illustrate the simple scalar function of Perl program PROCEDURE: PROGRAM: 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output $a=15, $b=5; $c=$a+$b; $d=$a*$b; $e=$a/$b; print "a is=$a\n"; print"b=$b\n"; print"the sum of two no.:$ c\n"; print"the multiplication:$ d\n"; print"the division:$e\n"; RESULT: The simple perl program that uses scalar was successfully executed and the output was saved 17

18 EXP. NO: 7 DATE: PERL SCRIPT USING <STDIN> AIM: To illustrate the use of <STDIN> PROCEDURE: 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output PROGRAM: print "Enter any number: "; $a=<stdin>; print "Enter another number: "; $b=<stdin>; $c=$a+$b; print "Addition of the numbers is: $c \n"; RESULT: The perl script that uses a <STDIN> Standard Input from user was successfully executed 18

19 EX.NO: 8 DATE: CHOP and CHOMP OPERATORS AIM: To illustrate two scalar variables one with \n character and other with only characters. PROCEDURE: PROGRAM: 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output $enzyme="ribonuclease\n"; chomp($enzyme); print"the gene after chomp function is :$enzyme\n"; $enzyme2= Helicase ; chop($enzyme2); print "the gene after chop operator is :$enzyme2\n"; print "Enter an enzyme name: ; $enzyme1=<stdin>; chomp($enzyme1); print "The entered gene after chomp function is:$enzyme1\n\n"; RESULT: The perl program that illustrates the Chop and Chomp operators was successfully executed 19

20 EX.NO: 9(a) DATE: AIM: To illustrate the if statement PROCEDURE: PERL CONTROL STATEMENTS IF STATEMENT 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output PROGRAM: print "Ente r a number below 10: "; $a=<stdin>; if( $a<10){ print "You entered correctly! \n"; } if( $a>=10){ print "You entered it wrong! \n"; } RESULT: The perl program that illustrated the if statement was successfully executed 20

21 IF ELSE STATEMENT AIM: To illustrate the use of if else statement. PROCEDURE: 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output PROGRAM: print Enter a number below 10: ; $a=<stdin>; if( $a<10){ print You entered correctly! \n ; } else{ print You entered it wrong! \n ; } RESULT: The perl program that illustrates the if else statement was successfully executed 21

22 EX.NO: 9(b) DATE: AIM: To illustrate the use of WHILE loop. PROCEDURE: PROGRAM: WHILE LOOP 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output print "Program to print first 10 natural numbers \n"; $i=1; while($i<=10){ print "$i \n"; $i++; } RESULT: The perl program that illustrates the while loop was successfully executed 22

23 DO WHILE LOOP AIM: To illustrate the use of DO WHILE loop. PROCEDURE: PROGRAM: 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output print "Program to print first 10 natural numbers \n"; $i=1; do{ print "$i \n"; $i++; } while($i<=10); RESULT: The perl program that illustrates the do while statement was successfully executed 23

24 EX.NO: 9(c) DATE: AIM: To illustrate the use of FOREACH LOOP. PROCEDURE: PROGRAM: FOREACH LOOP 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the Rahul Rehan); $count=1; foreach $names(@names){ print "$count $names \n"; $count++; } RESULT: The perl program that illustrates the foreach loop was successfully executed BI0313 / Perl Programming Laboratory 24

25 UNTIL AIM: To illustrate the UNTIL Loop PROCEDURE: PROGRAM: 1. Open Terminal, create a file using VI Editor and type in the program with.pl as extension 2. Compile and execute using #perl <filename.pl> command and note the output print "Program to print first 10 natural numbers \n"; $i=1; until( $i>10){ print "$i \n"; $i++; } RESULT: The perl program that illustrates the Until Loop was successfully executed 25

26 EX.NO: 10 DATE: SUBROUTINES AIM: To study and execute subroutines (sub programs) that is called in the main program # Any variable created outside a subroutine is Global and can be accessed inside subroutines. PROCEDURE: 1. Open Terminal and type the program in vi editor using subrout.pl command. 2. Execute the program and note the output. PROGRAM: print Enter degrees in Farenheit :\n ; $degf = <STDIN>; Chop($degf); print Celsius(); sub print celsius{ $degc = ($degf 32)*(5/9); print $degf degree farenheit is $degc degree celsius\n ; } 26

27 Subroutine using array and special variables PROGRAM: print "Enter any 5 numbers : \n"; $_= = split(); print "The sum is ",&sum_arr(@nums), "\n"; sub sum_arr{ my(@val) my(@sum) = 0; foreach $i(@val){ $sum = $sum + $i; } return ($sum); } RESULT: The programs that showed Subroutines and the use of arrays and special variables in subroutines was successfully executed and the output was saved 27

28 EX.NO: 11 DATE: RANDOM NUMBER GENERATION AIM: To generate a random integer/number using the rand() function. PROCEDURE: Open Terminal and type the program in vi editor, using vi rand.pl command. Execute and run to obtain a random number, use Ranges and obtain integers. Run by using perl rand.pl command, PROGRAM: Random number between 0 and 1 : use strict; use warnings; my $my_rand_num = rand(); print $my_rand_num. \n ; Range of numbers: use strict; use warnings; my $range = 100; $rand_num = rand($range); print $rand_num. \n ; 28

29 A random integer with a range: use strict; use warnings; my $range = 50; my $min = 100; my $rand_num = int(rand($range)) + $min; print $rand_num. \n ; RESULT: The perl program that illustrates the rand() function to generate random numbers was successfully executed 29

30 EX.NO: 12 DATE: PERL PROGRAMMING using FILE FUNCTIONS AIM: To study and execute a Perl program that uses functions to open and edit files. PROCEDURE: 1. Open Terminal and type the program in vi editor using file.pl command. 2. Execute the program Perl file.pl and note the output. PROGRAM: $path = "G:\Documents\123.seq"; open(handle, $path) or die "Error opening $path : $!"; $path = <HANDLE>; $a = ($path = ~tr/a//); $t = ($path = ~tr/t//); $g = ($path = ~tr/g//); $c = ($path = ~tr/c//); print "A is $a"; print "T is $t"; print "G is $g"; print "C is $c"; $total = $a + $t +$g +$c; print "Total number of nucleotides is $total \n"; 30

31 $gc = ((($g + $c)/ $total) *100); print GC content is :$gc \n ; close(handle); Formatting output with printf %.1f: To get one digit after the decimal (long float). ln program, printf GC content is :%.1f%\n,$gc; RESULT: The perl program that uses the functions such as open to view and edit files was successfully executed and the output was noted 31

32 EX.NO: 13 DATE: HASH TRAVERSAL FUNCTIONS Hashes are denoted by % AIM: To study and execute programs that shows the hash functions. PROCEDURE: 3. Open Terminal and type the program in vi editor using hashes.pl command. 4. Execute the program and note the output. PROGRAM: To traverse the hash and extract elements: print"program to print contents of a hash\n"; %coins=("quarter",25,"dime",10,"nickel",5); print"contents of the hash are:", %coins; Printing elements based on their key: print Program to print elements based on the key ; %coins = ( Quarter, 25, Dime, 10, Nickel, 5); foreach $key(%coins){ print {$key} \n ; } 32

33 To print the hash size: print Program to print hash size\n ; %coins = ( Quarter, 25, Dime, 10, Nickel, 5); print The hash size is :, scalar keys %coins; To add element to the hash: %coins = ("Quarter", 25, "Dime", 10, "Nickel", 5); print "Contents of the hash: ", %coins; $coins {"Penny"} = 1; print "\nafter addition: ",%coins; 33

34 To remove element from hash: %coins = ("Quarter", 25, "Dime", 10, "Nickel", 5); print "Contents of the hash: ", %coins; delete ($coins {"Quarter"}); print "\nafter deletion: ",%coins; To sort elements in the hash: %coins = ("Quarter", 25, "Dime", 10, "Nickel", 5); foreach $key (sort keys %coins){ print "{$key} \n"; } RESULT: All the perl programs that illustrated the hash traversal functions was successfully executed 34

35 EX.NO: 14 DATE: COMMAND LINE ARGUMENTS AIM: To study and execute the command line arguments using $#ARGV. PROCEDURE: 1. Open Terminal and type the program in vi editor. 2. Execute the program and note the output. PROGRAM: $numargs = $#ARGV + 1; print Thanks! You gave me $numargs command line arguments \n ; foreach $argnum(0..$#argv){ print $ARGV [$argnum] \n ; } RESULT: The perl program that illustrates Command line arguments was successfully executed. 35

36 EX.NO: 15 DATE: STDUID/STDGID PERL SCRIPTS AIM: To study and execute the stduid/stdgid file permissions using perl PROCEDURE: 1. Open terminal and type the program in a text editor, save with.pl extension 2. Execute and run the chmod file permissions command to obtain the output The long form of ls, ls l shows the stduid/stdgid programs by listing an s instead of /x When the stduid bit is turned on using the command chmod u+s stduid.pl, the privileges of the process are set to that of the owner/user of the file When the stdgid bit is turned on using the command chmod g+s stdgid.pl, the privileges of the process are set to that of the group of the file PROGRAM: print Welcome! This program sets file permissions \n ; In the TERMINAL: #ls l rw r r stduid.pl rw r r stdgid.pl #chmod a+x stduid.pl #ls l rwsr sr x stduid.pl #chmod g+x stdgid.pl #ls l rwsr sr x stdgid.pl 36

37 RESULT: The perl program that illustrates STDUID/STDGID perl scripts was successfully executed 37

38 EX.NO: 16 DATE: CREATING A STATIC HTML FILE AIM: To create and view the contents of a static html file using Perl programming. PROCEDURE: Open Terminal and type the program in vi editor using vi html.pl command. This creates a.html file in the root directory and can be viewed using a standard browser. Execute to create and run to view the html page. PROGRAM: Use Fentl; # The Module used for operations on file handles and i/o device handles, to read, extend attributes and control blocking etc. print Content type : text/html ; sysopen (HTML, myhtml.html, O_RDWR/O_EXCL/O_CREAT,0755); printf HTML <html>\n ; printf HTML <head>\n ; printf HTML <title>my Home Page!</title>\n ; printf HTML </head>\n ; printf HTML <body>\n ; printf HTML <palign = center >This is an HTML page</p> ; printf HTML </body>\n ; printf HTML </html>\n ; close (HTML); 38

39 Html file in the root has been created. Open: /root/myhtml.html file RESULT: A static HTML file using perl programming was successfully created. 39

Lecture # 2 Introduction to UNIX (Part 2)

CS390 UNIX Programming Spring 2009 Page 1 Lecture # 2 Introduction to UNIX (Part 2) UNIX is case sensitive (lowercase, lowercase, lowercase) Logging in (Terminal Method) Two basic techniques: 1. Network