BINF 634 Fall 2013 - Lecture 14 Review1

Final Review

Lec 1

• Review of Molecular Biology

– Central dogma

– Proteins

– DNA

– Reading frames

Perl topics:

• Running perl

• variables: scalars, arrays, hashes

• while loops

• Scalar and list context

• string operations

– printing

– substitution: s/x/y/

– translation: tr/abc/def/

Lec 2

• Input / output

• String operations

– concatentation, quoting

• String functions

– length, split, join, substr, index, sprintf, uc, lc, chomp

• Array Functions

• Conditionals

• Logical operators

• Loops

• Finding motifs

• Counting nucleotides

BINF 634 Fall 2013 - Lecture 14 Review2

Final Review

Lec 3

• Perl Shortcuts

• Declaring variables and Scope

• Subroutines

• Array References

• Programming Methods

– Top Down Design

– Bottom Up Coding and Testing

– Pseudocode

• Reading manuals and help pages

• Debugging

• POD

Lec 4

• Logical expression

• string functions: substr and index

• Random numbers and mutation

• Hashes

• Transcription, translation, genetic code

– Implementation using hashes

BINF 634 Fall 2013 - Lecture 14 Review3

Final Review

Lec 5

• Regular expressions

• Meta-characters

• Controlling patterns

– |, *, +, {N,M}, ?

• Capturing matches

– $`, $&, $'

– $1, $2 …

– ($x, $y) = $s =~ /(…) … (…)/

– g modifier

Lec 6

• Data Structures and Efficiency

• /usr/bin/time

• head, tail, diff, cmp

• Hashes for effiecient lookup and counting

– Intersection

– Unique items in two lists

– Counting items

• Sorting

– using BLOCKS

– using user-defined subroutinessort LISTsort BLOCK LISTsort USERSUB LIST

BINF 634 Fall 2013 - Lecture 14 Review4

Final Review

Lec 7

• Functions on arrays

– splice, grep, map

• Two-dimensional arrays

– Processing

– Printing

– Transposing

• Using Hashes to Pass Parameters to subroutines

Lec 8

• Perl Modules

• Module Getopt::Std• Range Operator

• Restriction Maps

• Parsing Rebase File

BINF 634 Fall 2013 - Lecture 14 Review5

Final Review

Lec 9

• CGI.pm

• Creating HTML pages with Perl

• Forms processing

• A general Web front end for Perl programs

• Security in CGI Programming

– Taint mode -T

– Untainting user supplied data

– Using external programs

• Permissions issued

– cgi-bin directory

– Using temporary directories

Lec 10: SQL and MySQL• Tables• Column Types and Properties• Keys, Indexes, and

AUTO_INCREMENT• The mysql client• Creating databases and tables• Inserting records• Selecting data• Using conditionals• Using LIKE and NOT LIKE• Sorting query results• Limiting query results• Updating data• Deleting data• Using functions• Perl DBI

BINF 634 Fall 2013 - Lecture 14 Review6

Final Review

Lec 11

• Data Visualization

– GD::Graph

– gnuplot

Lec 12

• Advanced SQL for Multiple Table Databases

– JOINS

• Objected Oriented Perl

– Objects

– Attributes

– Methods

– Classes

– Instances

• Intro to BioPerl

– Bio::Seq

– Bio::SeqIO

– Bio::DB::GenBank

– Bio::Perl

BINF 634 Fall 2013 - Lecture 14 Review7

Final Review

Lec 13

• Adding links to CGI script

• Command Line Perl

– perl -e

– perl -ne

– perl -ane

– BEGIN {}, END {}

• Environmental variables and the ENV hash

• Files and Directories

– opendir, readdir, closedir, mkdir, rmdir, chdir

– File test operators

-r -w -x -o -e -s -f -d

• Recursion

• XML

Lec 14

• Final Review

Course readings:

• Tisdall:

– Chapters 1-12

– Appendix B

• Wall:

– Chapters 1, 5, 26

– pp 579-584

– Ch 24: Common Practices (recommended)

BINF 634 Fall 2013 - Lecture 14 Review8

Final Review

• Take Home Final Exam

– No collaboration allowed on the exam.

– Due to me via email by 7:15 pm Monday 12/16/13

– No extensions will be given

– Good Luck!

1. Barplot in GD (See Visualization Lecture)

2. Barplots in GD on a Directory Structure (See Cmd Line Recursion Lecture)

3. Shaded Pattern in GD (See http://search.cpan.org/~lds/GD-2.46/GD.pm, think about the order that you draw things in)

4. PubMed XML Processing (See the Cmd Recursion Record)

5. File extraction and conversion with Bioperl (See Bioperl Lecture)

6. LWP (See http://search.cpan.org/~gaas/libwww-perl-6.03/lib/LWP.pm)

7. Bioperl Sequence Manipulations (See BioPerl Lecture)

8. Barplots in PDL see hint and visualization lecture

9. Piecharts in R see tonight’s lecture

10. Please try to provide me answers based on your real needs when possible.

Additional Reading

• Mastering Perl for Bioinformatics [Paperback]

– James D. Tisdall (Author)

• Building Bioinformatics Solutions: with Perl, R and MySQL [Paperback]

– Conrad Bessant (Author), Ian Shadforth (Author), Darren Oakley(Author)

BINF 634 Fall 2013 - Lecture 14 Review 9

Thanks to each and everyone of you to taking this course with me!

Perseverance is the hard work you do after you get tired of doing the hard work you already did.

Newt Gingrich

Read more at http://www.brainyquote.com/quotes/quotes/n/newtgingri1

07062.html#Ayx6LpiuIl4lAZfR.99

BINF 634 Fall 2013 - Lecture 14 Review 10

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BINF 634 Fall 2013 - Lecture 14 Review 11

Course Evaluation

• Evaluate my course by using the MyMason Portal listed below.  

– http://myMason.gmu.edu/

– Closing dates

• 12/10/11 regular sections

• 12/9/11 distance learning section

– Training slides are provided at the url below

• https://crserating.gmu.edu/CourseEvaluation.ppt

• The evaluations are important to me and the university.

• You must must use their Mason Net ID and password to access the system.

• The survey is not available between 6 pm on Sundays and 6 am on Mondays due to server maintenance.

BINF 634 Fall 2013 - Lecture 14 Review 12