Mastering Python for Bioinformatics

Spis treści ebooka

• Preface
  • Who Should Read This?
  • Programming Style: Why I Avoid OOP and Exceptions
  • Structure
  • Test-Driven Development
  • Using the Command Line and Installing Python
  • Getting the Code and Tests
  • Installing Modules
  • Installing the new.py Program
  • Why Did I Write This Book?
  • Conventions Used in This Book
  • Using Code Examples
  • OReilly Online Learning
  • How to Contact Us
  • Acknowledgments
• I. The Rosalind.info Challenges
• 1. Tetranucleotide Frequency: Counting Things
  • Getting Started
    • Creating the Program Using new.py
    • Using argparse
    • Tools for Finding Errors in the Code
    • Introducing Named Tuples
    • Adding Types to Named Tuples
    • Representing the Arguments with a NamedTuple
    • Reading Input from the Command Line or a File
    • Testing Your Program
    • Running the Program to Test the Output
  • Solution 1: Iterating and Counting the Characters in a String
    • Counting the Nucleotides
    • Writing and Verifying a Solution
  • Additional Solutions
    • Solution 2: Creating a count() Function and Adding a Unit Test
    • Solution 3: Using str.count()
    • Solution 4: Using a Dictionary to Count All the Characters
    • Solution 5: Counting Only the Desired Bases
    • Solution 6: Using collections.defaultdict()
    • Solution 7: Using collections.Counter()
  • Going Further
  • Review
• 2. Transcribing DNA into mRNA: Mutating Strings, Reading and Writing Files
  • Getting Started
    • Defining the Programs Parameters
    • Defining an Optional Parameter
    • Defining One or More Required Positional Parameters
    • Using nargs to Define the Number of Arguments
    • Using argparse.FileType() to Validate File Arguments
    • Defining the Args Class
    • Outlining the Program Using Pseudocode
    • Iterating the Input Files
    • Creating the Output Filenames
    • Opening the Output Files
    • Writing the Output Sequences
    • Printing the Status Report
    • Using the Test Suite
  • Solutions
    • Solution 1: Using str.replace()
    • Solution 2: Using re.sub()
  • Benchmarking
  • Going Further
  • Review
• 3. Reverse Complement of DNA: String Manipulation
  • Getting Started
    • Iterating Over a Reversed String
    • Creating a Decision Tree
    • Refactoring
  • Solutions
    • Solution 1: Using a for Loop and Decision Tree
    • Solution 2: Using a Dictionary Lookup
    • Solution 3: Using a List Comprehension
    • Solution 4: Using str.translate()
    • Solution 5: Using Bio.Seq
  • Review
• 4. Creating the Fibonacci Sequence: Writing, Testing, and Benchmarking Algorithms
  • Getting Started
    • An Imperative Approach
  • Solutions
    • Solution 1: An Imperative Solution Using a List as a Stack
    • Solution 2: Creating a Generator Function
    • Solution 3: Using Recursion and Memoization
  • Benchmarking the Solutions
  • Testing the Good, the Bad, and the Ugly
  • Running the Test Suite on All the Solutions
  • Going Further
  • Review
• 5. Computing GC Content: Parsing FASTA and Analyzing Sequences
  • Getting Started
    • Get Parsing FASTA Using Biopython
    • Iterating the Sequences Using a for Loop
  • Solutions
    • Solution 1: Using a List
    • Solution 2: Type Annotations and Unit Tests
    • Solution 3: Keeping a Running Max Variable
    • Solution 4: Using a List Comprehension with a Guard
    • Solution 5: Using the filter() Function
    • Solution 6: Using the map() Function and Summing Booleans
    • Solution 7: Using Regular Expressions to Find Patterns
    • Solution 8: A More Complex find_gc() Function
  • Benchmarking
  • Going Further
  • Review
• 6. Finding the Hamming Distance: Counting Point Mutations
  • Getting Started
    • Iterating the Characters of Two Strings
  • Solutions
    • Solution 1: Iterating and Counting
    • Solution 2: Creating a Unit Test
    • Solution 3: Using the zip() Function
    • Solution 4: Using the zip_longest() Function
    • Solution 5: Using a List Comprehension
    • Solution 6: Using the filter() Function
    • Solution 7: Using the map() Function with zip_longest()
    • Solution 8: Using the starmap() and operator.ne() Functions
  • Going Further
  • Review
• 7. Translating mRNA into Protein: More Functional Programming
  • Getting Started
    • K-mers and Codons
    • Translating Codons
  • Solutions
    • Solution 1: Using a for Loop
    • Solution 2: Adding Unit Tests
    • Solution 3: Another Function and a List Comprehension
    • Solution 4: Functional Programming with the map(), partial(), and takewhile() Functions
    • Solution 5: Using Bio.Seq.translate()
  • Benchmarking
  • Going Further
  • Review
• 8. Find a Motif in DNA: Exploring Sequence Similarity
  • Getting Started
    • Finding Subsequences
  • Solutions
    • Solution 1: Using the str.find() Method
    • Solution 2: Using the str.index() Method
    • Solution 3: A Purely Functional Approach
    • Solution 4: Using K-mers
    • Solution 5: Finding Overlapping Patterns Using Regular Expressions
  • Benchmarking
  • Going Further
  • Review
• 9. Overlap Graphs: Sequence Assembly Using Shared K-mers
  • Getting Started
    • Managing Runtime Messages with STDOUT, STDERR, and Logging
    • Finding Overlaps
    • Grouping Sequences by the Overlap
  • Solutions
    • Solution 1: Using Set Intersections to Find Overlaps
    • Solution 2: Using a Graph to Find All Paths
  • Going Further
  • Review
• 10. Finding the Longest Shared Subsequence: Finding K-mers, Writing Functions, and Using Binary Search
  • Getting Started
    • Finding the Shortest Sequence in a FASTA File
    • Extracting K-mers from a Sequence
  • Solutions
    • Solution 1: Counting Frequencies of K-mers
    • Solution 2: Speeding Things Up with a Binary Search
  • Going Further
  • Review
• 11. Finding a Protein Motif: Fetching Data and Using Regular Expressions
  • Getting Started
    • Downloading Sequences Files on the Command Line
    • Downloading Sequences Files with Python
    • Writing a Regular Expression to Find the Motif
  • Solutions
    • Solution 1: Using a Regular Expression
    • Solution 2: Writing a Manual Solution
  • Going Further
  • Review
• 12. Inferring mRNA from Protein: Products and Reductions of Lists
  • Getting Started
    • Creating the Product of Lists
    • Avoiding Overflow with Modular Multiplication
  • Solutions
    • Solution 1: Using a Dictionary for the RNA Codon Table
    • Solution 2: Turn the Beat Around
    • Solution 3: Encoding the Minimal Information
  • Going Further
  • Review
• 13. Location Restriction Sites: Using, Testing, and Sharing Code
  • Getting Started
    • Finding All Subsequences Using K-mers
    • Finding All Reverse Complements
    • Putting It All Together
  • Solutions
    • Solution 1: Using the zip() and enumerate() Functions
    • Solution 2: Using the operator.eq() Function
    • Solution 3: Writing a revp() Function
  • Testing the Program
  • Going Further
  • Review
• 14. Finding Open Reading Frames
  • Getting Started
    • Translating Proteins Inside Each Frame
    • Finding the ORFs in a Protein Sequence
  • Solutions
    • Solution 1: Using the str.index() Function
    • Solution 2: Using the str.partition() Function
    • Solution 3: Using a Regular Expression
  • Going Further
  • Review
• II. Other Programs
• 15. Seqmagique: Creating and Formatting Reports
  • Using Seqmagick to Analyze Sequence Files
  • Checking Files Using MD5 Hashes
  • Getting Started
    • Formatting Text Tables Using tabulate()
  • Solutions
    • Solution 1: Formatting with tabulate()
    • Solution 2: Formatting with rich
  • Going Further
  • Review
• 16. FASTX grep: Creating a Utility Program to Select Sequences
  • Finding Lines in a File Using grep
  • The Structure of a FASTQ Record
  • Getting Started
    • Guessing the File Format
  • Solution
  • Going Further
  • Review
• 17. DNA Synthesizer: Creating Synthetic Data with Markov Chains
  • Understanding Markov Chains
  • Getting Started
    • Understanding Random Seeds
    • Reading the Training Files
    • Generating the Sequences
    • Structuring the Program
  • Solution
  • Going Further
  • Review
• 18. FASTX Sampler: Randomly Subsampling Sequence Files
  • Getting Started
    • Reviewing the Program Parameters
    • Defining the Parameters
    • Nondeterministic Sampling
    • Structuring the Program
  • Solutions
    • Solution 1: Reading Regular Files
    • Solution 2: Reading a Large Number of Compressed Files
  • Going Further
  • Review
• 19. Blastomatic: Parsing Delimited Text Files
  • Introduction to BLAST
  • Using csvkit and csvchk
  • Getting Started
    • Defining the Arguments
    • Parsing Delimited Text Files Using the csv Module
    • Parsing Delimited Text Files Using the pandas Module
  • Solutions
    • Solution 1: Manually Joining the Tables Using Dictionaries
    • Solution 2: Writing the Output File with csv.DictWriter()
    • Solution 3: Reading and Writing Files Using pandas
    • Solution 4: Joining Files Using pandas
  • Going Further
  • Review
• A. Documenting Commands and Creating Workflows with make
  • Makefiles Are Recipes
  • Running a Specific Target
  • Running with No Target
  • Makefiles Create DAGs
  • Using make to Compile a C Program
  • Using make for a Shortcut
  • Defining Variables
  • Writing a Workflow
  • Other Workflow Managers
  • Further Reading
• B. Understanding $PATH and Installing Command-Line Programs
• Epilogue
• Index

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