BioCantor
A Python library that integrates flexible feature arithmetic with sequences and arbitrarily nested coordinate systems.
These core data models are then built upon to build in-memory representations of genomic intervals, including genes, transcripts and non-coding features.
These data structures can be parsed from GenBank and GFF3, and exported to GenBank, GFF3 and BED.
BioCantor arithmetic usage examples
BioCantor annotation model examples
- BioCantor Annotation Data Structures
- Annotation Object Model
- Parsing annotation files with BioCantor
- Parsing GenBank files
- Parsing GFF3 files
- Understanding Incorporating Variation
- Exporting BioCantor data models
- AnnotationCollection Operations
- Representing AnnotationCollections as JSON/dictionaries
- Chunk-relative coordinates