CSB472H1: Computational Genomics and Bioinformatics

Transcription

1 CSB472H1: Computational Genomics and Bioinformatics Tutorial #8 Alex Nguyen, 2014 ESC-4075

2 What we have seen so far Variables A way to store values into memories. Functions Print, string functions If/else, for, while Conditionals Comparisons Arrays and hashes Subroutines Regex Input/Output

3 Subroutines Code sharing is an important aspect of the community Algorithm modifications (Blast derivatives etc.) Problem: small number of programmers code in PERL. How to effectively transmit an algorithm?

4 Logic Algorithm overview can be given by logic charts Input initialization Procedure Condition False Output True

5 Formulas Algorithm description is often given as formulas For example Formulas are often the fastest way to get the point across. Formulas are preferred by the bioinformatics community, however they can lead to ugly notations: If($x == 1){return 5;} elsif($x == 0) {return 10;} 5 * (x) + 10 * (1-x) 5 x * 10 1-x

6 Pseudocodes Pseudocodes are code abstractions Pseudocodes are structured as codes, but are not meant to be interpreted by machines. Code-specific syntax can, and should, be left out When reading a pseudocode, I should not be able to say: It looks like PERL. Do not write: open(file,$filename); Spot all the problems

7 Pseudocodes Blocks should be clear Input: string a of length m, string b of length n F[0,0] := 0 structure d := penalty for all i: F[i,0] := -i * d Mathematics do not have to be explained for all j: F[0,j] := -j * d for i = 1 to m: for j = 1 to n: F[i,j] = max(f[i-1,j-1] + S[a[i],b[j]], F[i-1,j]-d,F[i,j-1]-d) There is no true standard for pseudocode syntax. KEEP IT CONSISTENT.

8 Pseudocodes The pseudocode has to provide enough information for: - Solving the problem in any programming language - The complete understanding of every variable used

9 Pseudocodes Class exercise (previously been an assignment) diff := Pa - Pb na := len(a) nb := len(b) if diff < 0 swap(a,b) swap(na,nb) diff := abs(diff) a[0.. 9] corresponds to the first ten letters of read a a[0.. 0] corresponds to the first letter of read a only a[na.. na] is empty where na is the length of a (remember 0 th index) Pa and Pb are in 0th index but this is not required abs() is the absolute value len() is the length of the read swap() exchanges the variables 3 rd position (0-index) in read_1 k := diff output_read := a[0.. diff-1] while k < na r1 := a[k.. k] r2 := b[k-diff.. k-diff] if r1!= "." output_read := output_read + r1 elsif r2!= "." and r2!= "" output_read := output_read + r2 else output_read := output_read + "." CA.TG..C.GT.G.T..AC.G..GA 1 rst position (0-index) in read_2 CA.TG.AC.GT.GA k := k + 1 output_read := output_read + b[na-diff.. nb-1]

10 What we have seen so far Variables A way to store values into memories. Functions Print, string functions If/else, for, while Conditionals Comparisons Arrays and hashes Subroutines Regex Input/Output Pseudocodes

11 Modules While code is often shared by pseudocode, the vast majority of coding languages contain libraries of code written by the community Modules are pieces of code that other people have written in your language In many cases, they will provide more efficient and broad case code.

12 Modules What can modules do? The community has coded a wide range of codes that you can take advantage of Manipulation of Window s mouse Writing Excel files Drawing images Complex mathematical functions

13 Modules Why shouldn t you use a module? Any module you use requires that anyone who uses your code have that module Some modules may not be trivial to install Some modules are incompatible with the user s Perl version If you code for specific cases, your code might be faster No easy way of modifying the function

14 Modules How to install modules

15 Modules It can take awhile to find the module you want It is maybe best you browse some forums and see what other people have used

16 Modules Perl modules require installation On Windows, this installation is done through PPM A nice interface should open called the Perl Package Manager

17 Modules Perl modules require installation On linux based OS You will have to type things instead both do practically the same thing Type: install packagename

18 Modules Let s install the Excel- Writer module

19 Modules Let s install the Excel- Writer module

20 Modules Let s install the Excel- Writer module

21 Modules Excel-Writer module done! How to use it?

22 Modules use Excel::Writer::XLSX; my $workbook = Excel::Writer::XLSX->new('test.xlsx'); my $worksheet = $workbook->add_worksheet(); for(my $i = 0;$i < 100;++$i){ $worksheet->write($i, 0, sqrt($i)); }

23 BioPERL Modules BioPERL is a collection of perl modules written by biologists Many of the tools you have learned about in class can be used via BioPERL You even have access to some algorithmic functions like the Needleman algorithm Installing BioPERL should be fairly straightforward

24 BioPERL Modules BioPERL is a collection of perl modules written by biologists

25 BioPERL Modules use Bio::SeqIO; my $file = "CSB assignment_1.fasta"; my $seqio_object = Bio::SeqIO->new(-file => $file); my $seq_object = $seqio_object->next_seq; print $seq_object->display_id; print "\n"; print $seq_object->seq; print "\n"; Automatic format recognition, automatic handling of files

26 Object Oriented programming OO programming vs procedural my $sub = substr($string,1,2); Subject Object oriented programming places the subject as the owner of the function my $sub = $string->substr(1,2); Note that this is not right. It is, however, how almost all modules work

27 Object Oriented programming Let s use BioPERL to create sequence objects. use Bio::Seq; use Bio::SeqIO; $seq_obj = Bio::Seq->new(-seq => 'atgcggctg', -display_id => 'new_dna', -desc => 'random_protein'); $seqio_obj = Bio::SeqIO->new(-file => 'test.fasta', -format => 'fasta'); $seqio_obj->write_seq($seq_obj);

28 Web programming Bioinformatics resources can usually be ran online User Interface Inputs Parameters Scripts and programs Output

29 Web programming A series of input/output programs User Interface Inputs Parameters Scripts and programs The output is usually interpreted by your browser (HTML code) Output

30 What we have seen this semester Variables %hashes. Functions If/else, for, while Conditionals Comparisons Subroutines Regex Input/Output Pseudocode BioPERL Command line arguments Web programming