Tutorial Contents

• Intro
  • A brief note on conventions
• Create a BedTool
• Intersections
• Saving the results
• Default arguments
• Chaining methods together (pipe)
• Operator overloading
• Intervals
  • Common Interval attributes
  • Indexing into Interval objects
  • Fields
  • BED is 0-based, others are 1-based
    • Worked example
  • GFF features have access to attributes
• Filtering
  • Fast filtering functions in Cython
• Each
• Using the history and tags
• Deleting temp files specific to a single BedTool