README.md

Implement contig contamination analysis as in (blog post)

gather-by-contig.py

#! /usr/bin/env python
"""
Walk through a file of long contigs and analyze each one for contamination
against an SBT database.

Author: C. Titus Brown, [email protected]

Requires sourmash 2.0.0a6.
"""
import argparse
import screed
import sourmash
from sourmash import sourmash_args, search
from sourmash.sbtmh import SearchMinHashesFindBestIgnoreMaxHash
import csv


def main():
    p = argparse.ArgumentParser()
    p.add_argument('input_seqs')
    p.add_argument('sbt_database')
    p.add_argument('--threshold', type=float, default=0.05)
    p.add_argument('--output-nomatch', type=argparse.FileType('wt'))
    p.add_argument('--output-match', type=argparse.FileType('wt'))
    p.add_argument('--csv', type=argparse.FileType('wt'))
    args = p.parse_args()

    tree = sourmash.load_sbt_index(args.sbt_database)
    print(f'found SBT database {args.sbt_database}')

    leaf = next(iter(tree.leaves()))
    mh = leaf.data.minhash.copy_and_clear()

    print(f'using ksize={mh.ksize}, scaled={mh.scaled}')

    print(f'loading sequences from {args.input_seqs}')
    if args.output_match:
        print(f'saving match sequences to {args.output_match.name}')
    if args.output_nomatch:
        print(f'saving nomatch sequences to {args.output_nomatch.name}')
    if args.csv:
        print(f'outputting CSV summary to {args.csv.name}')

    found_list = []
    total = 0
    matches = 0
    for record in screed.open(args.input_seqs):
        total += 1
        found = False
        search_fn = SearchMinHashesFindBestIgnoreMaxHash().search

        query_mh = mh.copy_and_clear()
        query_mh.add_sequence(record.sequence)
        query = sourmash.SourmashSignature(query_mh)

        # too small a sequence/not enough hashes? notify
        if not query_mh.get_mins():
            print(f'note: skipping {query.name()[:20]}, no hashes in sketch')
            continue

        for leaf in tree.find(search_fn, query, args.threshold):
            found = True
            matches += 1
            similarity = query.similarity(leaf.data)
            found_list.append((record.name, leaf.data.name(), similarity))
            break

        if not found:
            found_list.append((record.name, '', 0.0))

        if found and args.output_match:
            args.output_match.write(f'>{record.name}\n{record.sequence}\n')
        if not found and args.output_nomatch:
            args.output_nomatch.write(f'>{record.name}\n{record.sequence}\n')

        print(f'searched {total}, found {matches}', end='\r')

    print('')

    if args.csv:
        w = csv.DictWriter(args.csv, fieldnames=['query', 'match', 'score'],
                           delimiter='\t')
        w.writeheader()
        for (query, match, score) in found_list:
            w.writerow(dict(query=query, match=match, score=score))

if __name__ == '__main__':
    main()

requirements.txt

sourmash==2.0.0a6

I was trying to use this and noticed that the class SearchMinHashesFindBestIgnoreMaxHash from sourmash.sbtmh was actually GatherMinHashesFindBestIgnoreMaxHash.

Since December 2019 GatherMinHashesFindBestIgnoreMaxHash became GatherMinHashes see sourmash-bio/sourmash#556

Please see sourmash-bio/sourmash#941 - adding it into sourmash/ utils subdirectory now, so that it can be part of our tests!