MIE453 - Bioinformatics Systems (Fall 06)

Tutorial - Perl Debugging

Contents

1. Perl Debugger
2. Debugging using Eclipse-Perl Integration IDE

1. Perl Debugger

Perl debugger is similiar to many other line-oriented debuggers.

• Use the '-d' flag to run the debugger on the command line
• The debugger will halt at the first line of code that is to be executed
• The 'h' or 'h h' command will give you an outline of the available commands

Viewing the program code during execution

• The 'l' (list) command is used to display windows of the program's code.
  • Consecutive use of it will show consecutive windows
  • l x-y list the code between x and y
• The '.' command moves the current window back to the next line to be executed.
• The 'v' command lists the window immediately surrounding the current line.
• The /pattern/ command can be used to move forward and backward through the code to find regular expressions.

Executing code in the debugger

• The 'n' command runs until the next statement.
  • if the current line is a subroutine call, the debugger won't stop until returning from that subroutine.
• use the 's' (single-step) command to stop at the first line of the called subroutine.
• The 'r' command executes until returning from the current subroutine

Viewing variable values

• The 'p' command is to view the values of variables
• The 'x' command prints the variable in nicer format

Breakpoints

• The 'b' command (breakpoint) stop the execution at a certain line of code, or when a certain condition is met.
  • The simplest type of breakpoint is via a line number: b 24
  • Use the name of subroutine to break at the first line of the subroutine: b sub-name
• The 'L' command lists all of breakpoints that have been set so far
• The 'B' command clear all breakpoints
• The 'c' command (continue) runs the code until the next breakpoint
  • c nnn contines and stops at line nnn
• The 'w' command (watch) suspends the program when the value of a variable is changed.
  • e.g. w $arg
• The 'W' command clear all watches

Summary

List/search source lines:               
  l [ln|sub]  List source code
  - or .      List previous/current line
  v [line]    View around line
  f filename  View source in file
  /pattern/ ?patt?   Search forw/backw
  M           Show module versions
Debugger controls:
  o [...]     Set debugger options
  <[<]|{[{]|>[>] [cmd] Do pre/post-prompt
  ! [N|pat]   Redo a previous command
  H [-num]    Display last num commands
  = [a val]   Define/list an alias
  h [db_cmd]  Get help on command
  h h         Complete help page
  |[|]db_cmd  Send output to pager
  q or ^D     Quit

Control script execution:
  T           Stack trace
  s [expr]    Single step [in expr]
  n [expr]    Next, steps over subs
  <CR/Enter>  Repeat last n or s
  r           Return from subroutine
  c [ln|sub]  Continue until position
  L           List break/watch/actions
  t [expr]    Toggle trace [trace expr]
  b [ln|event|sub] [cnd] Set breakpoint
  B ln|*      Delete a/all breakpoints
  a [ln] cmd  Do cmd before line
  A ln|*      Delete a/all actions
  w expr      Add a watch expression
  W expr|*    Delete a/all watch exprs
  ![!] syscmd Run cmd in a subprocess
  R           Attempt a restart

Data Examination:     
  expr           Execute perl code, also see: s,n,t expr
  x|m expr       Evals expr in list context, dumps the result or lists methods.
  p expr         Print expression (uses script's current package).
  S [[!]pat]     List subroutine names [not] matching pattern
  V [Pk [Vars]]  List Variables in Package.  Vars can be ~pattern or !pattern.
  X [Vars]       Same as "V current_package [Vars]".  i class inheritance tree.
  y [n [Vars]]   List lexicals in higher scope .  Vars same as V.
  e              Display thread id     
  E              Display all thread ids.

Examples

• testDebugger.pl
• testArgs.pl
• ex1.pl
• ex2.pl

2. Debugging using Eclipse-Perl Integration IDE

In order to debug Perl program using this method you need to install

• Eclipse
• Eclipse Perl Integration (EPIC)

Demo

......

Examples in this tutorial is taken from http://www.emunix.emich.edu/%7Eevett/BioinformaticsTools/PerlDebugger.html and http://kobesearch.cpan.org/htdocs/perl/perldebtut.pm.html