torchcell.sequence

Genome and sequence data structures. Genome is the abstract genome interface (lazy gene-set and sequence access), Gene a gene within it, and DnaWindowResult and DnaSelectionResult the sequence windows the embedding datasets consume. torchcell.sequence.genome.base holds the organism-agnostic AnnotatedGenome (the recorded data.db cache, GO, gene-name resolution) that each host subclasses; the S. cerevisiae S288C implementation lives in torchcell.sequence.genome.scerevisiae, and torchcell.sequence.genome.registry resolves the sha256-pinned reference genome files.

Classes

DnaSelectionResult	A validated DNA region selection with coordinates, strand, and sequence.
DnaWindowResult	A DNA selection extended with the surrounding window coordinates.
Gene	Abstract gene exposing windowed-sequence extraction methods.
GeneSet	A sorted set that requires all members to be strings.
Genome	Abstract genome providing lazy gene-set and sequence access.
ParsedGenome	Validated container holding a genome's GeneSet.

Functions

calculate_window_bounds	Calculate the window bounds for genomic sequences.
calculate_window_bounds_symmetric	Calculate symmetric window bounds considering chromosome limits.
compute_codon_frequency	Compute relative codon frequencies for a coding sequence.
get_chr_from_description	Extracts the chromosome number from a given description string.
mismatch_positions	Computes the positions at which two sequences differ.
roman_to_int	Converts a Roman numeral string to an integer.