Bioinformatics programming using Python
Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be usin...
| Autor principal: | |
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| Formato: | Libro electrónico |
| Idioma: | Inglés |
| Publicado: |
Beijing ; Sebastopol, California :
O'Reilly Media
2010.
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| Edición: | First edition |
| Materias: | |
| Ver en Biblioteca Universitat Ramon Llull: | https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009628433806719 |
Tabla de Contenidos:
- Table of Contents; Preface; Introduction; About This Book; About Bioinformatics; About the Reader; Python; Some Context; The Python Language; Installing Python; Running Python; Notes; Reading and Reference Recommendations; Example Code; Unfortunate and Unavoidable Vocabulary Overlap; Comments; Conventions Used in This Book; We'd Like to Hear from You; Using Code Examples; Safari® Books Online; Acknowledgments; Chapter 1. Primitives; Simple Values; Booleans; Integers; Floats; Strings; Expressions; Numeric Operators; Logical Operations; String Operations; String operators; Subscription; Slicing
- CallsFunction calls; Method calls; Compound Expressions; Tips, Traps, and Tracebacks; Tips; Statements and expressions; Running Python interactively; Traps; Tracebacks; Chapter 2. Names, Functions, and Modules; Assigning Names; Defining Functions; Function Parameters; Comments and Documentation; Assertions; Default Parameter Values; Using Modules; Importing; Module namespaces; The random module; Python Files; Tips, Traps, and Tracebacks; Tips; Names; Function definitions; Executing code; Using IDLE; Managing Python files; Traps; Tracebacks; Chapter 3. Collections; Sets; Sequences
- Strings, Bytes, and BytearraysCreating; Testing; Searching; Replacing; Changing case; Reformatting; The format method and function; Ranges; Tuples; Tuple syntax; Tuple packing and unpacking; Lists; Statements that modify lists; List modification methods; Sequence-oriented string methods; Mappings; Dictionaries; Dictionary example: RNA codon translation table; Dictionary operations; Dictionary methods; Streams; Files; Creating file objects; File methods; Example; Generators; Collection-Related Expression Features; Comprehensions; List comprehensions; Set and dictionary comprehensions
- Generator expressionsConditional comprehensions; Nested comprehensions; Functional Parameters; The parameter "key"; Function objects; Anonymous functions; Tips, Traps, and Tracebacks; Tips; Language features; Developing and testing code; Traps; Tracebacks; Chapter 4. Control Statements; Conditionals; Loops; Simple Loop Examples; Initialization of Loop Values; Looping Forever; Loops with Guard Conditions; Iterations; Iteration Statements; Kinds of Iterations; Do; Collect; Combine; Search; Filter; Nested iterations; Recursive iterations; Exception Handlers; Python Errors; Tracebacks
- Runtime errorsException Handling Statements; Optional features of exception handling statements; Exception handling and generator objects; Raising Exceptions; The raise statement; Raising an exception to end a loop; Extended Examples; Extracting Information from an HTML File; The Grand Unified Bioinformatics File Parser; Reading the sequences in a FASTA file; Generalized parsing; Parsing GenBank Files; Translating RNA Sequences; Step 1; Step 2; Step 3; Step 4; Step 5; Constructing a Table from a Text File; Step 1; Step 2; Step 3; Step 4; Step 5; Tips, Traps, and Tracebacks; Tips; Traps
- Tracebacks
