Perl programming for biologists

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Title:

Personal Author:

Jamison, D. Curtis

Publication Information:

Hoboken, N.J. : Wiley-Liss, 2003

ISBN:

9780471430599

Subject Term:

Biology -- Data processing

Perl (Computer program language)

Available:*

Library	Item Barcode	Call Number	Material Type	Item Category 1	Status
Searching... PSZ JB	30000010062136	QH324.2 J36 2003	Open Access Book	Book	Searching... Unknown

Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that spare the rote repetition of code.

Author Notes

Curtis Jamison received his B.A. (Molecular, Cellular and Developmental Biology) from the University of Colorado, Boulder in 1985, and his Ph.D. (Biological Sciences) from the University of Denver in 1991. He held an NSF CISE postdoctoral fellowship while at National Center for Supercomputing Applications, University of Illinois, Champaign-Urbana, where he received a patent for his work on distributed application gateways and database federation. Dr. Jamison continued his work on database federation with plant genome databases for the USDA Agricultural Genome Information Service, and then later evolved to work on higher organisms at the National Institutes of Health where he created computational tools for genome mapping for the Human Genome Project. He is currently an Associate Professor of Bioinformatics at George Mason University, and is director of the Bioinformatics Ph.D. program.

Part I. The Basics	p. 1
Introduction	p. 3
Chapter 1. An Introduction to Perl	p. 7
1.1 The Perl Interpreter	p. 7
1.2 Your First Perl Program	p. 8
1.3 How the Perl Interpreter Works	p. 9
Chapter Summary	p. 10
For More Information	p. 11
Exercises	p. 11
Chapter 2. Variables and Data Types	p. 13
2.1 Perl Variables	p. 13
2.2 Scalar Values	p. 14
2.3 Calculations	p. 17
2.4 Interpolation and Escapes	p. 19
2.5 Variable Definition	p. 22
2.6 Special Variables	p. 23
Chapter Summary	p. 23
For More Information	p. 24
Exercises	p. 24
Programming Challenges	p. 24
Chapter 3. Arrays and Hashes	p. 27
3.1 Arrays	p. 27
3.3 Array Manipulation	p. 30
3.3.1 Push and Pop, Shift and Unshift	p. 30
3.3.2 Splice	p. 31
3.3.3 Other Useful Array Functions	p. 33
3.3.4 List and Scalar Context	p. 34
3.4 Hashes	p. 37
3.5 Maintaining a Hash	p. 38
Chapter Summary	p. 40
For More Information	p. 40
Exercises	p. 40
Programming Challenge	p. 41
Chapter 4. Control Structures	p. 43
4.1 Comparisons	p. 44
4.2 Choices	p. 45
4.2.1 If	p. 45
4.2.2 Boolean Operators	p. 46
4.2.3 Else	p. 47
4.3 Loops	p. 49
4.3.1 For Loops	p. 50
4.3.2 Foreach Loops	p. 52
4.4 Indeterminate Loops	p. 54
4.4.1 While	p. 54
4.4.2 Repeat Until	p. 56
4.5 Loop Exits	p. 57
4.5.1 Last	p. 57
4.5.2 Next and Continue	p. 57
Chapter Summary	p. 59
Exercises	p. 59
Programming Challenges	p. 60
Part II. Intermediate Perl	p. 61
Chapter 5. Subroutines	p. 63
5.1 Creating a Subroutine	p. 63
5.2 Arguments	p. 64
5.3 Return	p. 65
5.3.1 Wantarray	p. 66
5.4 Scope	p. 67
5.4.1 My	p. 67
5.5 Passing Arguments with References	p. 70
5.6 Sort Subroutines	p. 71
Chapter Summary	p. 73
For More Information	p. 74
Exercises	p. 74
Programming Challenges	p. 74
Chapter 6. String Manipulation	p. 75
6.1 Array-Based Character Manipulation	p. 75
6.2 Regular Expressions	p. 78
6.2.1 Match	p. 79
6.2.2 Substitute	p. 81
6.2.3 Translate	p. 81
6.3 Patterns	p. 82
6.3.1 Atoms	p. 83
6.3.2 Special Atoms	p. 83
6.3.3 Quantifiers	p. 84
6.3.4 Assertions	p. 85
6.3.5 Alternatives	p. 85
Chapter Summary	p. 86
For More Information	p. 87
Exercises	p. 87
Programming Challenges	p. 87
Chapter 7. Input and Output	p. 89
7.1 Program Parameters	p. 89
7.2 File I/O	p. 90
7.2.1 Filehandles	p. 90
7.2.2 Working with Files	p. 91
7.2.3 Built-in File Handles	p. 92
7.2.4 File Safety	p. 93
7.2.5 The Input Operator	p. 94
7.2.6 Binary I/O	p. 97
7.3 Interprocess Communications	p. 97
7.3.1 Processes	p. 98
7.3.2 Process Pipes	p. 98
7.3.3 Creating Processes	p. 99
7.3.4 Monitoring Processes	p. 100
7.3.5 Implicit Forks	p. 101
Chapter Summary	p. 102
For More Information	p. 102
Exercises	p. 102
Programming Challenges	p. 103
Chapter 8. Perl Modules and Packages	p. 105
8.1 Modules	p. 105
8.2 Packages	p. 107
8.3 Combining Packages and Modules	p. 109
8.4 Included Modules	p. 110
8.4.1 CGI	p. 110
8.4.2 Getopt	p. 110
8.4.3 Io	p. 112
8.4.4 File::Path	p. 112
8.4.5 Strict	p. 113
8.5 The CPAN	p. 114
8.5.1 Setting Up the CPAN Module	p. 114
8.5.2 Finding Modules	p. 115
8.5.3 Installing Modules	p. 117
8.5.4 Managing Installed Modules	p. 119
Chapter Summary	p. 121
For More Information	p. 121
Exercises	p. 121
Programming Challenges	p. 122
Part III. Advanced Perl	p. 123
Chapter 9. References	p. 125
9.1 Creating References	p. 125
9.2 ref()	p. 126
9.3 Anonymous Referents	p. 127
9.4 Tables	p. 128
Chapter Summary	p. 130
Exercises	p. 130
Programming Challenge	p. 130
Chapter 10. Object-Oriented Programming	p. 133
10.1 Introduction to Objects	p. 133
10.1.1 The OOP Approach	p. 134
10.1.2 Class Design	p. 135
10.1.3 Inheritance	p. 136
10.2 Perl Objects	p. 136
10.2.1 Rule Number One	p. 137
10.2.2 Rule Number Two	p. 137
10.2.3 Rule Number Three	p. 138
10.2.4 Methods	p. 139
10.2.5 Constructors	p. 141
10.2.6 Accessors	p. 143
10.2.7 OOP Versus Procedural	p. 143
Chapter Summary	p. 145
For More Information	p. 146
Exercises	p. 146
Programming Challenges	p. 146
Chapter 11. Bioperl	p. 147
11.1 Sequences	p. 147
11.2 SeqFeature	p. 149
11.3 Annotation	p. 150
11.4 Sequence I/O	p. 151
11.5 Cool Tools	p. 152
11.6 Example Bioperl Programs	p. 154
11.6.1 Primer.pl	p. 154
11.6.2 Primer3.pm	p. 156
Chapter Summary	p. 161
For More Information	p. 161
Exercises	p. 161
Programming Challenges	p. 162
Appendix A. Partial Perl Reference	p. 163
Chapter 3	p. 163
Chapter 4	p. 163
Chapter 5	p. 164
Chapter 6	p. 164
Chapter 7	p. 164
Chapter 8	p. 165
Chapter 9	p. 165
Appendix B. Bioinformatics File Formats	p. 167
GenBank	p. 167
ASN.1	p. 170
EMBL	p. 175
PDB	p. 177
Fasta	p. 181
BLAST	p. 182
ACEDB	p. 183
Index	p. 185

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