1. 13.1 Wrapping up

2. 13.2 Running Other Programs

3. 13.3 You may run programs using the system function: $exitValue = system("blastall.exe..."); if ($exitValue!=0) {die "blast failed!";} This way the output of blast will be seen on the screen. You can use ' > ' to redirect the output to a file: $exitValue = system("blastall.exe... > out.blast"); If you want to capture the output use “back-ticks” (left of the “1” key on your keyboard): @blastOutput = `blastall.exe...`; In this case the output of blast is stored in the array. Running programs from a script

4. 13.4 e.g. Rate4Site: Still not very widely used (174 citations so far…) so there is no BioPerl modules that will run it for you and read its output:Rate4Site Dealing with less common formats #POS SEQ SCORE QQ-INTERVAL STD MSA DATA #The alpha parameter 1.5 1 K -0.9763 [-1.6621,-0.5750] 0.8777 6/6 2 V 0.9820 [-0.1107,2.2169] 1.5983 6/6 3 F 0.0035 [-0.9640,0.4935] 1.3195 6/6 4 S 0.2010 [-0.7766,0.8962] 1.3975 6/6 5 K -0.3480 [-1.1423,0.1673] 1.0990 6/6 6 C -0.7887 [-1.4855,-0.3560] 1.0182 6/6 7 E -0.9894 [-1.6621,-0.5750] 0.8714 6/6 8 L 0.0153 [-0.9640,0.4935] 1.3378 6/6 9 A -1.1347 [-1.6621,-0.7766] 0.7487 6/6 10 H -0.3200 [-1.1423,0.1673] 1.1252 6/6 11 K -0.3557 [-1.1423,0.1673] 1.1077 6/6 12 L -0.8331 [-1.4855,-0.3560] 0.9965 6/6 13 K -0.9763 [-1.6621,-0.5750] 0.8777 6/6 14 A 1.6809 [0.4935,2.2169] 1.6672 6/6 15 Q 1.4315 [0.1673,2.2169] 1.7297 6/6 16 E 0.1025 [-0.9640,0.8962] 1.3784 6/6 17 M 0.5006 [-0.5750,1.4226] 1.4456 6/6

5. 13.5 1. You could install blast on your computer from: ftp.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov (There go to the directory: blast/executables/release/) But this may be difficult, and you will also need to download and install the databases you want to search. 2. You can also work on the Unix servers of the bioinformatics unit you can use local blast that is already installed there. Genbank databases that are installed there can be used for blast and for any other work, such as getting a sequence by its accession. Running a local blast

6. 13.6 Some Final Notes

7. 13.7 BioPerl issues If you are having problems installing BioPerl on your computer, you might need to add a repository to PPM. We've added instructions to the course webpage. BioPerl warnings about: Subroutine... redefined at... Should not trouble you too much.

8. 13.8 Referencing array : $gradesRef = \@grades; $arrayRef = [85,91,67]; Referencing hash : $phoneBookRef = \%phoneBook; $hashRef ={"pupko"=>7693, "lab" =>9245 }; Referencing - Dereferencing Dereferencing array : @arr = @{$arrRef}; $element1 = $arrRef->[0]; Dereferencing hash : %hash = %{$hashRef}; $myVal = $hashRef->{"myKey"}; @grades $gradesRef $phoneBookRef %phoneBook => $arrRef $hashRef =>

9. 13.9 Really final notes Ex. 6 has been updated (some clarification added). If and when you use PERL in your after-course life, we will be glad to help you along the way.

10. 13.10 The Exam

11. 13.11 The exam will take place on 14/07/2009 at 09:00 – 12:00. Material of the exam: everything. The exam will be on the computers in computer classrooms all around the campus (arrive early!! to find your class). Entry to the class will be on 08:50. The computers will be disconnected from the network (i.e. no internet access. Sorry… ). There will be files waiting on the computer which you will use during the exam, and the exam questionnaire on paper. You will write your solutions as normal Perl scripts. At the end of the exam we will collect your scripts.

12. 13.12 The following software will be on the computers: –ActivePerl –Perl Express –Regex Coach –Eclipse – If you want to have Eclipse let us know before the exam by email! You are allowed to bring 2 (double sided) A4 pages. You may use the Perl documentation in Perl Express (Press the button with the purple book on the left panel, or in the menu: Help  Perl Documentation)

13. 13.13 Perl function documentation in PerlExpress

14. 13.14 2.(10pts) Write a script in the file named "exam2.pl" that asks the user to enter a number n and then a list of numbers, separated by spaces. Print every n’th number. For example: If the user enters “3” and “1 2 3 4 5 6 7 8 9 10” the script should print "3 6 9". Exam questions from 2008

15. 13.15 3.(20pts) Write regular expressions to match the following patterns below. Save only the regular expressions in the file "exam3.txt" (don’t write a script there) b. Find this motif in a protein sequence: G, followed by any 5 amino acids, followed by one or two A's, followed by T or S. Match both upper-case and lower-case letters. c. Match a reference line in a GenBank file, such as this example: RL EMBO J. 10:2879-2887(1991). It must start with "RL", followed by the abbreviation of the journal name, followed by the volume number, followed by the pages, followed by a 4-digit year. Your expression should extract the two page numbers separately – "2879" and "2887" in the above example. Exam questions from 2008

16. 13.16 5.(20 pts) The file “exam5.pl” contains a script that reads a blast output file (see for example “blast.txt”). The script should find all hit lines, such as this one: >ref|NT_039586.4 Mus musculus chromosome 13, strain C57BL The hit lines always start with ">". Also, blast was run against the mouse genome so all hit lines include "chromosome i" (i is the chromosome number). Note that this script should ignore hits to the X & Y chromosomes! a.The script should store the count of the number of hits for every chromosome in the array @chroms, using the chromosome number as the index in the array (cell number 0 will not be used). So, for example, if there were 2 hits to chromosome 1 and 5 hits to chromosome 2, than the array should be: (0,2,5) Fill in the missing lines 21-22 and 28-29. Save this version of the script as “exam5a.pl” Exam questions from 2008