Programming Languages and Uses in Bioinformatics

Transcription

1 Programming in Perl

2 Programming Languages and Uses in Bioinformatics Perl, Python Pros: reformatting data files reading, writing and parsing files building web pages and database access building work flow pipelines can write scripts quickly; good for one-time use scripts Cons: higher memory usage slower calculation performance Java Pros: building applications with graphical user interfaces (GUI) Very fast at calculations such as sequence alignments good for developing long term use applications like Agilent Genomic Workbench low memory usage Cons: requires more time to write C,C++ Pros: Very fast at calculations such as sequence alignments low memory usage Cons: requires more time to write

3 Programming Development approach write a small chunk of code run it knowledge applied loop knowledge acquired loop any errors? yes fix errors no If I can fail six times a minute, I ll acquire knowledge six times faster than a programmer who fails only once every minute. Greg Voss, Polymorphic C Dr. Dobb s Journal, August 1994

4 script starts from line 1 Program Execution Basics

5 Programming in Perl cd mkdir genomics_lab/ws2 cd genomics_lab/ws2 # go to your home directory # create a directory called ws2 # go to your ws2 directory gedit hello_world.pl & # create a file called hello_world.pl # & sends process to the background #!/usr/bin/perl print Hello World!\n ; # first line lets UNIX know that this is a Perl script # print is a Perl function # \n is the new line character Save your file and exit gedit UNIX commands Perl Perl scripts scripts

6 ls l #show the permissions for all files permissions - user group size date_modified file and directory names rw rw r 1 genomics genomics 6 Jan 29 22:07 hello_world.pl Directories show up as blue font non-executable files show up as white font d = directory - = file user group other r = read w = write x = execute drwxr xr x whoami groups # show your user name # show all groups you belong to

7 Change the permissions of your hello_world.pl script to executable chmod +x hello_world.pl # change mode to executable rwxr xr x 1 genomics genomics 6 Jan 29 22:07 hello_world.pl Directories show up as blue font Executable files show up as green font Now run your script from the UNIX command line (Terminal) using either of these two commands perl hello_world.pl./hello_world.pl

8 Variables in Perl Variables are used to hold data. Different data types use different variable types. There are three data structures in Perl: scalar, array and hash You should use a variable name that is informative of its contents. Use lowercase characters and separate words with underscore character. scalar variables starts with $ and holds a single unit of data containing text, numbers,... $percent_gc = 85.3; $day = Monday ; $book_title = The cat in the hat ; $today = $day; $percent_gc = ;

9 Using scalar variables in Perl gedit hello_world.pl & # edit your hello_world.pl script #!/usr/bin/perl -w $my_name = Michael ; print Hello $my_name!\n ; # use -w to turn on warnings # $my_name is a variable that is assigned # the value: Michael Now run your script from the UNIX command line (Terminal)./hello_world.pl

10 Using arguments in Perl gedit hello_world.pl & # edit your hello_world.pl script #!/usr/bin/perl -w $my_name = shift; print Hello $my_name!\n ; # use -w to turn on warnings # $my_name is a variable that is assigned # the value of the argument Now run your script from the UNIX command line and use your name as an argument./hello_world.pl Michael

11 for Loops for loops are used to loop through designated blocks code i.e. executing a block of code a specified number of iterations gedit hello_world_loops.pl & # create a new script #!/usr/bin/perl -w $i = shift 1; for (1.. $i) { $loop = $_; print $loop\thello World!\n ; # is syntax for an OR condition # defaults to 1 if no argument is given # $i is often used for iteration # $_ is a Perl reserved variable which contains what iteration the loop is on # \t is to insert a tab in the output chmod +x hello_world_loops.pl # make your script executable Now run your script from the UNIX command line and use a number as an argument./hello_world_loops.pl 9

12 Conditional statements if (condition) { code; # (condition) is either TRUE or FALSE # TRUE = 1 # FALSE = 0 if (condition) { code; elsif (different condition) { different code; if (condition) { code; else { other code; if (condition) { code; elsif (different condition) { different code; else { other code;

13 Assignment vs Conditional statements use one = sign $number = 1; # you are assigning a value of 1 to $number if ($number == 1) { # you are comparing $number to the value of 1 use two == signs #!/usr/bin/perl -w $number = 1; if ($number == 1) { print Number equals 1 \n ; else { print Number does not equal 1 \n ;

14 Comparison Operators == comparing if numeric values are equal eq comparing if text strings are the same!= comparing if numeric values are not equal ne comparing if text strings are not the same Other numeric comparisons > >= < <= What is the symbol for not greater than?!>

15 Write a script to output the following using a for loop from 1 to 10 and conditional statements five ten #!/usr/bin/perl -w for (1.. 10) { if ($_ == 5) { print five\t ; elsif ($_ == 10) { print ten ; else { print $_\t ; print \n ;

16 length( ) function in Perl #!/usr/bin/perl -w #this script will evaluate the length of a DNA sequence $dna_sequence = GAGTCGAATCGT ; $dna_length = length($dna_sequence); #get DNA length if ($dna_length > 10) { print DNA sequence is longer than 10 bases.\n ; elsif ($dna_length < 10) { print DNA sequence is shorter than 10 bases.\n ; else { print DNA sequence is 10 bases long.\n ; comments about your script begin with # and can be placed on a line by themselves or at the end of a line of code

17 substr( ) function in Perl substr position counting starts at 0 $dna_sequence = GCATCGAATCGT ; position substr($dna_sequence, 1, 3); # will give you CAT #!/usr/bin/perl -w $dna_sequence = GCATCGAATCGT ; #start at $dna_sequence character 0 and get 1 character(s) $first_nucleotide = substr($dna_sequence, 0, 1); if ($first_nucleotide eq G ) { print G is the first base in the DNA sequence.\n ; else { print G is not the first base in the DNA sequence.\n ;

18 Logical Expressions is the syntax for OR && is the syntax for AND if ($nucleotide eq G ) { $gc_count = $gc_count + 1; elsif ($nucleotide eq C ) { $gc_count = $gc_count + 1; # we can combine two conditions to make our code more concise Logical OR syntax (two pipes with no space) if ($nucleotide eq G $nucleotide eq C ) { $gc_count = $gc_count + 1; Now this line is needed only once.

19 Logical Expressions is the syntax for OR && is the syntax for AND Logical AND syntax (two & characters with no space) #!/usr/bin/perl -w $chromosome = 1; $gene_start = ; if ($chromosome == 1 && $gene_start >= ) { print Your gene is on the q arm of chromosome 1\n ;

20 script to get RNA transcript of your DNA #!/usr/bin/perl -w #This script will transcribe DNA to RNA $dna_sequence = GCATCGAATCGT ; $dna_length = length($dna_sequence); #get DNA length for (0.. ($dna_length - 1)) { $nucleotide = substr($dna_sequence, $_, 1); if ($nucleotide eq T ) { print U ; else { print $nucleotide ; print \n ;

21 exit # exit the terminal session; Ctrl+d

22 To be completed before next class Write a script to get %GC of a DNA sequence get the DNA sequence as a command line argument print the percent GC hints: increment a value each time a nucleotide matches all of these lines of code do the same calculation $gc_count = $gc_count + 1; $gc_count += 1; $gc_count++; Make sure you understand the following Perl functions and variables: for (1.. 10) \n && if $_ \t elsif else == substr( ) eq length( )