API Reference¶

dot-explorer exposes its functionality through the following classes and functions.

Classes¶

Class	Module	Description
`SequenceIndex`	`dot_explorer`	Rust-backed rolling-hash k-mer index for sequence comparison
`DotPlotter`	`dot_explorer.dotplot`	All-vs-all dotplot visualisation
`CrossIndex`	`dot_explorer.paf_io`	Multi-group cross-index for cross-group pairwise comparisons; DotPlotter-compatible
`PafRecord`	`dot_explorer.paf_io`	Single PAF alignment record
`PafAlignment`	`dot_explorer.paf_io`	Collection of PAF records with reordering utilities; DotPlotter-compatible

Function	Module	Description
`py_read_fasta`	`dot_explorer`	Read a FASTA or gzipped FASTA file
`py_build_kmer_set`	`dot_explorer`	Build the k-mer set for a sequence
`py_find_kmer_coords`	`dot_explorer`	Find k-mer positions in a sequence via FM-index
`py_merge_runs`	`dot_explorer._dot_explorer`	Unified strand-aware merge: forward and both RC patterns
`py_merge_kmer_runs`	`dot_explorer`	Merge forward-strand (`+`) co-linear k-mer hits into blocks
`py_merge_rev_runs`	`dot_explorer._dot_explorer`	Merge RC anti-diagonal k-mer hits (standard inverted repeat)
`py_merge_rev_fwd_runs`	`dot_explorer._dot_explorer`	Merge RC co-diagonal k-mer hits (both arms same direction)
`py_coords_to_paf`	`dot_explorer`	Convert coordinate tuples to PAF lines
`py_save_index`	`dot_explorer`	Serialise an index collection to disk
`py_load_index`	`dot_explorer`	Load a serialised index from disk
`parse_paf_file`	`dot_explorer.paf_io`	Yield PAF records from a file
`compute_gravity_contigs`	`dot_explorer.paf_io`	Sort contigs by best-chromosome gravity centre; report reverse-oriented contigs
`compute_reversed_contigs`	`dot_explorer.paf_io`	Detect reverse-oriented query contigs (d-genies orientation check)
`reverse_complement`	`dot_explorer.paf_io`	Reverse-complement a nucleotide string