UNIX and Perl to the Rescue!

Part I. Introduction and Background: 1. Introduction; 2. How to use this book; Part II. Installing Unix and Perl: 3. What do I need in order to learn Unix and Perl?; 4. Installing Linux on a PC; 5. Installing a code editor; Part III. Essential Unix: 6. Introduction to Unix; 7. The Unix terminal; 8. The Unix command prompt; 9. Your first Unix command; 10. The hierarchy of a Unix file system; 11. Finding out where you are in the filesystem; 12. How to navigate a Unix filesystem; 13. Absolute and relative paths; 14. Working with your home directory; 15. The Unix shell; 16. Environment variables; 17. Introduction to command-line options; 18. Main pages; 19. Working with directories; 20. The importance of saving keystrokes; 21. Moving and renaming files; 22. Moving and renaming directories; 23. How to remove files; 24. How to copy files and directories; 25. Working with text files; 26. Introduction to aliases; 27. Editing text files; 28. Automating Unix commands; 29. How to hide filesand find hidden files; 30. Creating a configuration file; 31. Programming with Unix; 32. Unix file permissions; 33. How to specify which directories contain programs; 34. Creating useful shell scripts; 35. Unix summary; Part IV. Essential Perl: 36. Hello world; 37. Scalar variables; 38. Use warnings; 39. Maths and functions; 40. Perl vs perl; 41. Conditional statements; 42. Use strict; 43. Stopping programs; 44. Working with strings; 45. Dealing with special characters; 46. Matching operators; 47. The transliteration operator; 48. List context; 49. Introduction to arrays; 50. Array manipulation; 51. The @ARGV array; 52. Defined and undefined variables; 53. Sorting; 54. Introduction to loops; 55. More loops; 56. Loop control; 57. Data input and output; 58. Reading and writing files; 59. Introduction to hashes; 60. Working with hashes; 61. Introduction to regular expressions; 62. Regular expression metacharacters; 63. Working with regular expressions; 64. Interacting with other programs; 65.

Keith Bradnam is a project scientist in the Genome Center at the University of California, Davis. He has extensive experience working with model organism databases and spent four years as a project leader at WormBase, helping to develop this important bioinformatics resource. Ian Korf is an Associate Professor in Molecular and Cellular Biology at the University of California, Davis. His research seeks to understand structure and function in genomic DNA. He has developed new tools for gene prediction, co-authored the only book devoted to BLAST and helped in the development of BioPerl.