University:
Boston University
Course:
GRS CS 910 | Directed Study: Systems
Academic year:

2022
Views:

109

Pages:

17
Author:

Jimena Kerr

Code Examples Walk Through Code Examples Examples To walk through: (code examples are in ./code/session1/) 1. bio_nts_trans.pl - example in real world to show regular expression in use 2. bio_prot_trans.pl – example in real world to show hash structure in use Let’s go to the terminal to go through these examples now. Packages and Modules Purpose of Packages/Modules • To address the complicity of software functionality, when single script is not sufficient and clear to provide the service. • It’s a way to organize code What is Package • ‘package’ – the term used for functionality, means a division of global namespace; can be spread across several files (modules); • It’s a logical unit for code functionality; • Declares the BLOCK or the rest of the compilation unit as being in the given namespace (Perldoc definition) • Package = Namespace (simplified) • Way Perl uses to implement ‘class’ (object-oriented) What is Module • ‘module’ – a library file consists of a set of related methods; • It can be used as ‘class’ definition or class implementation , or both (for example: Bio::SeqIO) • modules are actual physical libraries stored in file system to implement desired functioning system • the common practice is to organize them by their logical namespaces (package) Package vs Module - relationship • Modern design of perl modules – one module one package • object-oriented • hierarchically origanized, so outer namespace could cover the inner namespace, to provide modularity • Module file directory reflects namespace hierarchy • well defined interfaces between modules (namespaces); • Two Examples, Bio::DB and Bio::SeqIO Bio::DB – no common interface; every sub namespace is self-referenced Bio::SeqIO – has common abstract interface defined (implemented), while inside every sub namespace related to certain SeqIO may refer to this common interface BioPerl on SCC This is the first level file structure of BioPerl installed on SCC: for full library structure, refer to : doc/bioperl_structure.txt Perl help system Perl Language Reference • This is the ultimate resource of authority – BLUEPRINT of a language; • May be found too difficult to be understood for beginners ‘perldoc’ utility • Embedded Perl documentation system in ‘POD’ (Plain Old Documentation) format • Mostly written for Perl library modules: perldoc perldoc # how to use perldoc perldoc perlintro # perl introduction for beginners perldoc perltoc # Perl table of contents perldoc perl # overview of Perl perldoc perlfunc # Full list of Perl functions perldoc -f print # help on built-in function called ‘print’ perldoc perlop # full list of perl operators ‘man’ command • Linux ‘man’ command can be used to access perl module help, for example: man perl man perldoc man perltoc man perlre … • ‘perldoc’ is recommended over ‘man’ – ‘man’ depends on if the man pages are installed for certain Perl Modules or not Perl debugger perl -d • Use ‘perl –d scriptname’ to start debugger • Perl debugger is a fully integrated part to Perl interpreter, that means code must first pass the compiling process to be able to use debugger • Frequently used debugger commands: h: type the help information n: execute next statement s: single step execution r: start/restart/continue run the code b: set breakpoints v: view source code in the context Data::Dumper • Perl module commonly used to print out the variable structure and value; but more convenient • Usage: use Data::Dumper qw(Dumper); print Dumper \@an_array; print Dumper \%a_hash; print Dumper $a_reference; Data::Dumper Code Example