Beginning Perl for Bioinformatics. Steven Nevers Bioinformatics Research Group Brigham Young University

Transcription

1 Beginning Perl for Bioinformatics Steven Nevers Bioinformatics Research Group Brigham Young University

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3 Why Use Perl? Interpreted language (quick to program) Easy to learn compared to most languages Designed for working with text files Free for all operating systems Most popular language in bioinformatics

4 Perl s Disadvantages Richness and compactness of language facilitates difficult-toread programs No stand alone programs without additional software Slower to compiled code Perl cannot handle as large problems as some other programming languages

5 Programming In Perl, the program (script) is just a text file. Code it in any text editor Lower overhead (quick and dirty solutions)

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7 Hello World! The 'Hello World' example is the traditional incantation to the programming gods and will ensure your quick mastery of the language.

8 Print Almost all programming languages use print to mean write this to the console (command line) Once upon a time, the console was a typewriter. But now print never means print on a printer. print statements are necessary to keep tabs on what your program is doing You need to tell Perl to put a carriage return at the end of a printed lin Use \n in a text string to signify a newline.

9 Program details Perl programs on UNIX start with a line like: #!/usr/bin/perl Perl ignores anything after a # (the above command is to the UNIX shell). Elsewhere in the program # is used to indicate comments to explain the code Lines that are Perl commands end with a semicolon (;).

10 Run your Perl program Edit program vi Hello_World.pl Run program perl Hello_World.pl

11 Strings In Perl, strings are very important. They are just a series of any text characters-- letters, numbers In the statement print Hello, world\n ; } This part is the string

12 Numbers The other common type of data is a number. Perl can handle numbers in most common formats, without complications: E-26 Arithmetic functions + (add) - (minus) / (divide) * (multiply) ** (exponentiation)

13 A program using numbers Program #!/usr/bin/perl print 2+2\n ; print 3*4, \n ; print 8/2=, 8/2, \n ; Output /2=4

14 Variables Three basic types of variables in Perl Scalars: prefixed with $ e.g. $num Arrays: prefixed Hashes: prefixed with % e.g. %hashtable

15 Comparing strings String comparison (i.e. is the text the same?) eq (equal) ne (not equal) There are others but beware of them!

16 Getting part of a string substr takes characters out of a string which string where in the string how many letters to take

17 Example 4-1 Storing DNA in a variable, and printing it out

18 Example 4-2 Concatenating DNA

19 Example 4-3 Transcribing DNA into RNA

20 Example 4-4 Calculating the reverse complement of a strand of DNA

21 Example 4-5 Reading protein sequence data from a file

22 Example 4-6 Reading protein sequence data from a file, take 2

23 Example 4-7 Reading protein sequence data from a file, take 3

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25 Regular expression a specific pattern that provides concise and flexible means to match Several examples of the string car in a word (cartoon, bicarbonate) isolated (car) preceded by another word (motor car)

26 Basic matching Given: $mystring = Hello world! ; Does the string contain the word World? if($mystring =~ m/world/) {print Yes ; } No. The binding operator =~ with the match operator m// does a pattern search on $mystring and returns true if the pattern is found. Does the string contain the word World, ignoring case? if($mystring =~ m/world/i) {print Yes ; } Yes. The pattern modifier i immediately after the trailing / changes the match to be case-insensitive.

27 Basic substitution I want Hello world~ to be changed to Hello mom! instead. $mystring =~ s/world/mom/ print $mystring; It now prints Hello mom!

28 Common tasks How do I extract everything between the words start and end? Prints text always precedes the end of the. The pattern.* is two different metacharacters that tell Perl to match everything between the start and the end. Specifically, the metacharacter. means match any symbol except new line. The pattern quantifier * means match zero or more of the preceding symbol.

29 Common tasks, continued How do I extract everything between start and the first end encountered? Prints text always precedes the. By default, the quantifiers are greedy. This means that when you say.*, Perl matches every character (except new line) all the way to the end of the string, and then works backwards until it finds end. To make the pattern quantifier miserly, you use the pattern quantifier limiter?. This tells Perl to match as few as possible of the preceding symbol before continuing to the next part of the pattern.

30 Thank you! These slides and all example code are posted at: