Sassy is a library and tool for approximately searching short patterns in texts, the problem that goes by many names:
- approximate string matching,
- pattern searching,
- fuzzy searching.
The motivating application is searching short (~20bp) DNA fragments in a human genome (3GB), but it also works well for longer patterns up to ~1Kbp, and shorter texts.
> cargo run -r -- --help
Usage: sassy <COMMAND>
Commands:
search Default search behavior
crispr CRISPR-specific search with PAM and edit-free region
query Search multiple queries from a FASTA file against a target FASTA file
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
To search a single pattern (i.e. ACTGCTACTGTACA) in a fasta file
To find matches of a pattern with up to 1 edit:
cargo run -r -- search --alphabet dna ACTGCTACTGTACA 1 hg.faOutput is written as tab-separated values to stdout, containing the sequence id, distance, strand, start and end position, matched substring, and cigar string. (For matches to the reverse-complement strand, the query is reversed and matches are reported in the forward direction.)
chr1 2 + 74462851 74462868 ATCGGTGTCATCAATAA =D11=X4=
chr1 2 + 97381917 97381934 ACTCGGTGTCCTCATAA 10=X2=D4=
chr1 2 + 196285921 196285938 actggtgtcatcggtaa 3=D10=X3=
chr1 2 - 199471583 199471601 TTATCGATGACACTGAAT 13=X2=X=
chr1 2 - 229999068 229999085 ATATCGATGACACCAGT X13=D3=
chr1 2 - 231082126 231082144 ttatcaatgacaacgagt 5=X6=X5=
When searching a multi-fasta against another (multi) fasta file. For example to search a list of protospacers in a contig collection.
To find all spacer matches with up to 3 edits
cargo run -r -- query --alphabet iupac spacers.fasta 3 contigs.fastaThree alphabets are supported:
- ASCII: only equal characters match.
- DNA: Only
ACTGandactgcharacters are expected, and treated case-insensitively. - IUPAC: On top of the DNA characters, also supports
NYRand furter characters (again, case insensitive), so thatAmatchesN.
