README.md

Simple demonstration code to load sequences, compute signature, and do a search against an SBT.

sourmash compute --scaled 10000 -f data/GCF*.fna.gz
sourmash index -k 31 test.sbt GCF*.sig

./build-and-search.py test.sbt data/GCF_000005845.2_ASM584v2_genomic.fna.gz

build-and-search.py

#! /usr/bin/env python
from __future__ import print_function

import sys
import screed
import sourmash_lib

KSIZE=31

SBT_filename = sys.argv[1]

# get a DNA sequence somehow
query_seq = next(iter(screed.open(sys.argv[2]))).sequence
print('got {} DNA characters to query'.format(len(query_seq)))

# load an SBT; see sourmash_args.py for add'l load stuff, like checking ksize
tree = sourmash_lib.load_sbt_index(SBT_filename)

# build/load a signature
minhash = sourmash_lib.MinHash(ksize=KSIZE, n=0, scaled=10000)
minhash.add_sequence(query_seq)

query_sig = sourmash_lib.SourmashSignature('', minhash,
                                           name='my favorite query')

# do the search --
threshold = 0.1

for found_sig, similarity in sourmash_lib.search_sbt_index(tree, query_sig,
                                                           threshold):
    print((query_sig.name(), found_sig.name(), similarity,))