Module feature_match 

Sequence identity for the feature library: a feature’s bases in its own direction, a strand-independent key, and exact occurrences on both strands (wrapping on circles).

Structs

Occurrence

One exact occurrence of a query on a molecule.

Searcher

Repeated find_exact searches on one molecule, preparing the origin-wrapped text once.

Functions

canonical

Strand-independent identity: the lexicographically smaller of a sequence and its reverse complement. None for non-ACGT input.

feature_sequence

The feature’s bases 5′→3′ in its own direction: parts joined in source order, each wrapping through the origin if it does; reverse features are reverse-complemented. None if any base is not A, C, G or T.

find_exact

Every exact occurrence of query (ACGT, 5′→3′) on both strands, ordered by start then strand. A palindromic query is reported once, on the forward strand. On a circle, occurrences may run through the origin; a query longer than the molecule never matches.

reverse_complement

Watson–Crick complement of an upper-case ACGT sequence, read 5′→3′; None for any other base.

semiglobal_edits

Fewest substitutions, insertions and deletions that align all of short to some stretch of long (end gaps in long are free), or None if more than max.

translate_standard

Standard-code translation of whole codons from the first base (stops as *).