How-to pages

These pages explain pyranges1 functionalities grouped by topic:

• Loading/Creating PyRanges
  • From a DataFrame
  • From a Dictionary
  • Loading from a file
  • Concatenating PyRanges
  • Data for testing
• Writing to disk
  • Writing genomic formats
  • Writing tabular formats
• Inspecting PyRanges
  • String representation
  • Detecting invalid PyRanges
  • Column summary statistics
• Rows operations
  • Indexing with iloc, loc
  • Using boolean indexers
  • Using PyRanges .loci
  • Sorting PyRanges
• Columns operations
  • Fetching or writing a column
  • Extracting multiple columns
  • Dropping columns
• Working with sequences
  • Fetching sequences per interval
  • Fetching sequences per mRNA
  • Filtering by sequence
  • Translation and reverse complement
• Operating on coordinates
  • Operating on coordinates: cheatsheet
  • Modifying coordinates
  • Extending intervals
  • Slicing operations
  • Interval complement
  • Other slicing operations
• Overlap-related operations
  • Overlap-related operations: cheatsheet
  • Single and pairwise PyRanges operations
  • Methods for pairs of PyRanges
    • Filter rows: overlap
    • Common arguments: slack, strand_behavior, match_by
    • The most versatile: join_overlaps
    • Set operations: set_intersect_overlaps, set_union_overlaps
    • Interval manipulation operations: intersect_overlaps, subtract_overlaps
    • Fast counting: count_overlaps
    • Find the closest interval: nearest_ranges
  • Methods for single PyRanges
    • Grouping overlapping intervals: cluster_overlaps
    • Resolve overlaps: merge_overlaps, split_overlaps, max_disjoint_overlaps
• Mapping between coordinate systems
  • Mapping coordinate systems: cheatsheet
  • Nested coordinate systems
  • Mapping from local to global ranges
  • Mapping from global to local ranges