Mastering Python for bioinformatics : how to write flexible, documented, tested Python code for research computing

Mastering Python for bioinformatics how to write flexible, documented, tested Python code for research computing

Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals an...

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Detalles Bibliográficos
Otros Autores: Youens-Clark, Ken, author (author)
Formato: Libro electrónico
Idioma:Inglés
Publicado: Sebastopol : O'Reilly Media, Incorporated May 2021.
Materias:
Bioinformatics.
Python (Computer program language)
Python (Llenguatge de programació)
Bioinformàtica.
Ver en Biblioteca Universitat Ramon Llull:https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009631359706719
Tabla de Contenidos:
  • Preface
  • Part I. The Rosalind.info Challenges
  • Chapter 1. Tetranucleotide Frequency: Counting Things
  • Chapter 2. Transcribing DNA into mRNA: Mutating Strings, Reading and Writing Files
  • Chapter 3. Reverse Complement of DNA: String Manipulation
  • Chapter 4. Creating the Fibonacci Sequence: Writing, Testing, and Benchmarking Algorithms
  • Chapter 5. Computing GC Content: Parsing FASTA and Analyzing Sequences
  • Chapter 6. Finding the Hamming Distance: Counting Point Mutations
  • Chapter 7. Translating mRNA into Protein: More Functional Programming
  • Chapter 8. Find a Motif in DNA: Exploring Sequence Similarity
  • Chapter 9. Overlap Graphs: Sequence Assembly Using Shared K-mers
  • Chapter 10. Finding the Longest Shared Subsequence: Finding K-mers, Writing Functions, and Using Binary Search
  • Chapter 11. Finding a Protein Motif: Fetching Data and Using Regular Expressions
  • Chapter 12. Inferring mRNA from Protein: Products and Reductions of Lists
  • Chapter 13. Location Restriction Sites: Using, Testing, and Sharing Code
  • Chapter 14. Finding Open Reading Frames
  • Part II. Other Programs
  • Chapter 15. Seqmagique: Creating and Formatting Reports
  • Chapter 16. FASTX grep: Creating a Utility Program to Select Sequences
  • Chapter 17. DNA Synthesizer: Creating Synthetic Data with Markov Chains
  • Chapter 18. FASTX Sampler: Randomly Subsampling Sequence Files
  • Chapter 19. Blastomatic: Parsing Delimited Text Files
  • Appendix A. Documenting Commands and Creating Workflows with make
  • Appendix B. Understanding $PATH and Installing Command-Line Programs
  • Epilogue.

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