PERL PROGRAMMING FOR BIOLOGISTS
CONTENTS PART I THE BASICS INTRODUCTION CHAPTER 1 AN INTRODUCTION TO PERL THE PERL INTERPRETER YOUR FIRST PERL PROGRAM HOW THE PERL INTERPRETER WORKS CHAPTER SUMMARY FOR MORE INFORMATION EXERCISES CHAPTER 2 VARIABLES AND DATA TYPES PERL VARIABLES SCALAR VALUES CALCULATIONS INTERPOLATION AND ESCAPES VARIABLE DE?NITION SPECIAL VARIABLES PROGRAMMING CHALLENGES CHAPTER 3 ARRAYS AND HASHES ARRAYS ARRAY MANIPULATION PUSH AND POP, SHIFT AND UNSHIFT SPLICE OTHER USEFUL ARRAY FUNCTIONS LIST AND SCALAR CONTEXT HASHES MAINTAINING A HASH PROGRAMMING CHALLENGE CHAPTER 4 CONTROL STRUCTURES COMPARISONS CHOICES BOOLEAN OPERATORS ELSE LOOPS FOR LOOPS FOREACH LOOPS INDETERMINATE LOOPS WHILE REPEAT UNTIL LOOP EXITS LAST NEXT AND CONTINUE PART II INTERMEDIATE PERL CHAPTER 5 SUBROUTINES CREATING A SUBROUTINE ARGUMENTS RETURN WANTARRAY SCOPE PASSING ARGUMENTS WITH REFERENCES SORT SUBROUTINES CHAPTER 6 STRING MANIPULATION ARRAY-BASED CHARACTER MANIPULATION REGULAR EXPRESSIONS MATCH SUBSTITUTE TRANSLATE PATTERNS ATOMS SPECIAL ATOMS QUANTI?ERS ASSERTIONS ALTERNATIVES CHAPTER 7 INPUT AND OUTPUT PROGRAM PARAMETERS FILE I/O FILEHANDLES WORKING WITH FILES BUILT-IN FILE HANDLES FILE SAFETY THE INPUT OPERATOR BINARY I/O INTERPROCESS COMMUNICATIONS PROCESSES PROCESS PIPES CREATING PROCESSES MONITORING PROCESSES IMPLICIT FORKS CHAPTER 8 PERL MODULES AND PACKAGES MODULES PACKAGES COMBINING PACKAGES AND MODULES INCLUDED MODULES CGI GETOPT FILE::PATH STRICT THE CPAN SETTING UP THE CPAN MODULE FINDING MODULES INSTALLING MODULES MANAGING INSTALLED MODULES PART III ADVANCED PERL CHAPTER 9 REFERENCES CREATING REFERENCES REF() ANONYMOUS REFERENTS TABLES CHAPTER 10 OBJECT-ORIENTED PROGRAMMING INTRODUCTION TO OBJECTS THE OOP APPROACH CLASS DESIGN INHERITANCE PERL OBJECTS RULE NUMBER ONE RULE NUMBER TWO RULE NUMBER THREE METHODS CONSTRUCTORS ACCESSORS OOP VERSUS PROCEDURAL CHAPTER 11 BIOPERL SEQUENCES SEQFEATURE ANNOTATION SEQUENCE I/O COOL TOOLS EXAMPLE BIOPERL PROGRAMS PRIMERPL PRIMER3PM