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Perl Programming (Web-Published Since 2018)

Perl Template

• Template file for coding Perl (EBKim, Since 2024.10.23). [Download]

Perl Books and Tutorials

• [Book] Beginning Perl by Simon Cozens (PDF) [Visit]
• [Book] Modern Perl (2014. Edited by Shane Warden) (PDF) [Visit] [PDF]
• OOP in Perl. [Web] [PDF]
• [Book] BioPerl Tutorial - a tutorial for bioperl by Peter Schattner (PDF) [PDF]
• [WebBook] BioPerl - Beginners HOWTO [Visit]
• [온라인Book] Perl VS Python 코드 비교. [Web] [PDF]

Video Clips for Perl and Bioinformatics

• YouTube Channel - Perl and Bioinformatics [YouTube]

Installing a Perl Module 1 (In linux bash)

• 0. Install C and C++ Compilers (in Ubuntu, gcc, g++).
  sudo apt-get install gcc g++ build-essential
• 1. If you like to install XXX::YYY module in Ubuntu,
  sudo cpan XXX::YYY

Installing a Perl Module 2 (CPAN mode)

• 0. Install C and C++ Compilers (in Ubuntu, gcc, g++).
  sudo apt-get install gcc g++ build-essential
• 1. Enter CPAN by typing cpan.
• 2. If you like to install XXX::YYY module in CPAN, use the following command in the CPAN mode (cpan[1]>)
  install cpan XXX::YYY
• 3. Sometime, if you should install CPAN itselt in CPAN, use the follwing command in the CPAN mode (cpan[1]>)
  install CPAN

Installing a Perl Module 3 (Manual Installation)

• 1. Install C and C++ Compilers (in Ubuntu, gcc, g++).
  sudo apt-get install gcc g++ build-essential
• 2. Download a compressed module file from https://metacpan.org. [Web]
• 3. Extract source files from the compressed module file.
• 4. Move to the working folder.
• 5. Run a perl script by typing "perl Makefile.PL".
• 6. Build by typing "gmake" or "dmake" or "make"(for MacOS).
• 7. Copy built files to a library folder by typing "gmake install" or "dmake install" or "sudo make install"(for MacOS as a super user).

Perl Info

• Summary of Regular Expressions. [PDF]

Perl - Basic Level

• Data Types (Scalar, Array, and Hash) - By Eun Bae Kim [Web]
• Conditional Stetments (if, elsif, and else) - By Eun Bae Kim [Web]
• Loops (for and while) - By Eun Bae Kim [Web]
• File Handling (Open, Split, @ARGV) - By Eun Bae Kim [Web]
• Functions - Pre-Defined (sort, min/max, lc/uc, length, arrays) - By Eun Bae Kim [Web]
• Functions - User-Defined Subroutine - By Eun Bae Kim [Web]
• Regular Expression (Basics and Applications) - By Eun Bae Kim [Web]

Perl - 2nd Level

• Perl one-liners: CLI에서 파일처리를 짧은 코드로 처리할 때 유용. [TXT]
• Double Hash for 2D Table and Reference - By Eun Bae Kim [Web]
• Array Handling for map, grep, and uniq. [PPT]
• Call by Reference - Examples (by EBKim). [ZIP]

Perl for Fun

• Game - Rock Scissor Paper - By Eun Bae Kim [Web]
• Game - Find out the Number - By Eun Bae Kim [Web]
• Beep Music - Mount Rabbit - By Eun Bae Kim [Web]

Perl Application 1

• DNA Utility (Reverse Complement, GC Content, Translation) - By Eun Bae Kim [Web]
• Data Filtering (Array, Hash, Keys/Values) - By Eun Bae Kim [Web]
• Table Sorting based on Hashes - By Eun Bae Kim [Web]
• How to use SQLite3 - By Eun Bae Kim [Web]

Perl Application 2

• Statistics with R - By Eun Bae Kim [Web]
• URL Download, Genus/Species Counting - By Eun Bae Kim [Web]
• Fasta Handling - By Eun Bae Kim [Web]
• GenBank Handling 1 (Accession Number), Exception - By Eun Bae Kim [Web]
• GenBank Handling 2 (File, Tabulate), glob (File Array) - By Eun Bae Kim [Web]
• GenBank Handling 3 - Multiple Exons - By Eun Bae Kim and SEKim. [Web] [gbk]
• PubMed Medline - Download - By Eun Bae Kim [Web]
• PubMed Medline - Parsing - By Eun Bae Kim [Web]
• Protection of PDF File with a Password - By Eun Bae Kim [Web]

Perl Application 3

• Parallel Processing - By Eun Bae Kim [Web]
• Parallel Processing - Multiple-Level Hash - By Eun Bae Kim [Web]

Perl Simulation

• Monte Carlo - Calculating PI - By Eun Bae Kim [Web]

Perl Math

• Decimal Number to Binary Number - By Eun Bae Kim [Web]
• Ant Array (개미수열) - by EBKim [ZIP]

Perl Korean Letters

• Hangul Processing - Part 1 (Korean Letters) - by Eun Bae Kim [Web]
• Hangul Processing - Part 2 (Korean Letters) - By Eun Bae Kim [Web]