113-1_Perl_1_Introduction_to_command_line.pdf
- 1. Perl computer programming for bioinformatics You-Yu Lin
- 2. What is Perl? • General purpose programming language • Developed by Larry Wall, a linguist working as a systems administrator for NASA in the late 1980s, as a way to make report processing easier Larry Wall The Camel Book (de facto reference book for Perl) The Llama book (for beginners)
- 3. Development of Perl • Perl 1.0 was released in 1988 • Perl 5.000 was released in 1994 • Perl 5.36 released 2022/05/28 • Perl 6 was released in 1995 but renamed to Raku in 2019 • Perl 7 scheduled for release in 2023 but since cancelled (compatibility issues)
- 4. Why learn Perl? 1. Similar to other languages (C, shell script, python), easy to learn • Python was released in 1991 2. Easy and direct • Code is brief and effective • A lot of “Do-What-I-Means” 3. Useful and fast • Text processing • Web programming, GUI programming, bioinformatics, etc. 4. Free and resourceful • Large social community and online resources
- 5. Why not to learn Perl? 1. Too flexible…TIMTOWTDI (There Is More Than One Way To Do It) • Each person will have their own unique style, may be difficult for others and especially beginners to read 2. IP concerns • Perl is an interpreted language and your codes do not need compilation • Which also means very difficult to distribute your software without revealing your code
- 6. Where to get Perl? • Should be included with Unix/Linux or macOS systems • For Windows, https://www.perl.org/get.html • Strawberry Perl or ActiveState Perl
- 8. Your first Perl script • Enter 「print “Hello Worldn”;」 into a text file • Name file as 01_Hello.pl • File extension of Perl scripts are .pl • Not strictly required • However, will be recognized as Perl scripts and display with Perl-specialized coloring scheme • To execute the script, type 「perl -w 01_Hello.pl」in command line window script.pl script.txt
- 9. Say hello~~
- 10. Perl and Bioinformatics • Has been extensively used for data processing of sequencing data, which is essentially endless strings • The human TERT gene (NG_009265.1) is 48,881 bp long (TERT.fas includes first 350 bp as an example)
- 11. Enter the following code and execute it
- 12. The Perl code reads the input file (TERT.fas) and outputs it Potential manipulations to the input file • Translate to amino acid sequence • Identify exons and introns • Calculate CG content and codon frequencies • Compare homology with other sequences • More…
- 13. BioPerl • First released in 1995 • Contributed significantly for the Human Genome Project • Collection of bioinformatic-related Perl modules
- 14. PuTTY • Free and open source terminal software • https://www.putty.org/ • You do not have to use PuTTY, but you need a terminal interface to connect to a Linux server • Please prepare a working terminal interface before next class