1. Perl Programming Dr Claire Lambert
MSc Bioinformatics
Perl Programming Dr Claire Lambert

2. Data Types Scalars Arrays of scalars
Associative arrays of scalars (hashes)

3. Literals
Never changes - fixed
number
string
array
associative array

4. Variables Can change within the program number string array
associative array

5. Operators Addition Subtraction Multiplication Division + or += - or -=

6. Logical operators AND OR NOT true AND true then true
false OR false then false
NOT
changes state
true becomes false
false becomes true

7. Relational operators Equality Comparison Numeric Strings == , !=
eq , ne
Comparison
<, <=, >, >=, <=>
lt, le, gt, ge, cmp

8. You should now be able to
Setup appropriate data structures
define different types and give examples
illustrate operators that can be used
write perl programs

9. Programming style Good programming principles correctness efficiency
transparency, readability
modifiablity
robustness
documentation

10. Programming style Importance of criteria
depends on problem
circumstances in which program is written
environment in which program is to be used
correctness has highest priority
other criteria usually equal weight

11. Programming style Common mistake start writing immediately
use stepwise refinement
top down design
top level - algorithm
bottom level - primitive statements

12. Programming style Why conform to conventions? reduce risk of errors
produce programs
readable
easy to understand
easy to debug
easy to modify or extend

13. Programming style Good style rules short statements
procedures, functions, modules
good naming of data objects
layout for readability

14. Programming style Comments under-commenting over-commenting
main purpose
enable user
to use program
to understand program
to modify program

15. Programming style Comments what program does? how it is run
execution time and memory requirements
limitations
special system requirements
functions and arguments
implementation information

16. Programming style Efiiciency execution time space requirements
improvements
deeper understanding of problem
better programming
perl interpreter
execution efficiency
compilers are better at this

17. You should now be able to
Describe good programming principles (criteria)
the importance of the criteria
identify common mistakes made
explain why conform to style
identify good rules of style
why use comments, examples
identify areas of efficiency

18. Debugging Debugging Debugger getting rid of errors
syntax and logical
Debugger
tool to allow control when executing the program
breakpoints
print variable values

19. Debugging Syntax errors Common syntax errors compile-time errors
error message generated
Common syntax errors
missing semi-colon
string terminator “
errors not always on line specified
errors may not be related to message generated

20. Debugging Logical errors Perl -w filename.pl Debugger bugs
extra warnings
unused variables (typo)
variables used before they are set
Debugger
trace, breakpoints and actions
print variable values

21. Debugging Strict forces declaration of variables
does not allow mis-referencing

22. Debugging Debugger DB<1> a [line] ACTION b [line] L d [line]
X variable
s and n
c [line]

23. You should now be able to
Define what debugging is
identify types of errors and common errors
explain command line option -w
use strict to force variable declaration
use a debugger for a perl program