Using Pyokit

• Importing Pyokit modules
• Building user interfaces with Pyokit
  • The CLI class
  • The Option class
• Genomic Intervals
  • Processing BED files
    • Iterating over BED files
      • The basic BED iterator
      • The paired BED iterator
    • Bulk-loading BED files
      • Loading into a list
      • Loading into an interval tree
  • Manipulating Genomic Intervals
    • Collapsing interval sets
    • Intersecting interval sets
    • Searching interval sets
• Biological Sequences
  • Processing Fasta files
  • Processing FastQ files
  • Manipulating sequences
• Sequence Alignments
  • Pairwise alignments
    • Pairwise Alignment Meta-data
    • Reading and writing pairwise alignments
• Retrotransposons
  • Loading annotations
    • Repeatmasker coordinate annotation
    • Repeatmasker full alignments
    • Repeatmasker annotations with on-demand full alignments
  • Liftover
    • Coordinate-only liftover
    • Full-alignment liftover
• Gene Ontology
• File indexes