Topical Documentation

This section contains additional documentation not covered in the tutorial.

• Design principles
  • Principle 1: Temporary files are created (and deleted) automatically
  • Principle 2: Names and arguments are as similar as possible to BEDTools
  • Principle 3: Indifference to BEDTools version
  • Principle 4: Sensible default args
  • Principal 5: Other arguments have no defaults
  • Principle 6: Chaining together commands
  • Principle 7: Check the help
• Creating a BedTool
• Saving BedTool results
  • Use the BedTool.saveas() method
  • Use the BedTool.moveto() method
  • Use the output keyword argument
  • Working with non-interval output files
• Using BedTool objects as iterators/generators
  • Creating a BedTool from an iterable
  • Indexing a BedTool
• Low-level operations
• Working with BAM files
• Notes on BAM file semantics
• Specifying genomes
  • As a file
  • As a string
  • As a dictionary
  • Converting to a file
• Randomization
  • Example workflow
  • Other statistics
• Wrapping new tools
  • Example program description
  • Method name
  • Define a method in BedTool
  • Add the _wraps() decorator
  • Add doctests
  • Add to list of known programs
  • Summary
• Comparisons
• Shell script comparison
  • pybedtools version (py_ms_example.py)
  • bash version (sh_ms_example.sh)
• pybedtools development model
• Under the hood
  • Iterator “protocol”
    • Filename-based
    • Open file-based
    • Iterator or generator-based
  • Calling BEDTools programs