def test_searchfiles_contigs_just_search(location):
prefix = os.path.join(location, "pref")
filelist = [
f"{prefix}.contigs.ranksearch.csv",
f"{prefix}.contigs.ranksearch.matches.sig",
f"{prefix}.contigs.search.csv", f"{prefix}.contigs.search.matches.sig",
f"{prefix}.contigs.unmatched.fq"
]
sf = SearchFiles(prefix, search=True, gather=True)
# two minhashes, share ranks at phylum level
hashval = 12345678
ident1 = 'first'
mh1, sig1, lin1 = make_sig_and_lin([hashval], ident1, 'a;b;c')
hashval2 = 87654321
ident2 = 'second'
mh2, sig2, lin2 = make_sig_and_lin([hashval2], ident2, 'a;b;f')
# create lca_db w sigs
lca_db = LCA_Database(scaled=1, ksize=3)
lca_db.insert(sig1, ident=ident1)
lca_db.insert(sig2, ident=ident2)
# make lin_db
lin_db = LineageDB()
lin_db.insert(ident1, lin1)
lin_db.insert(ident2, lin2)
num_hashes = 2
# search with combined hashvals
search_mh = make_mh([hashval, hashval2])
results, rank_results = search_containment_at_rank(search_mh, lca_db,
lin_db, "class")
gather_results = list(gather_at_rank(search_mh, lca_db, lin_db, "class"))
#write search results
name = 'name'
seq_len = 6
for res in results:
sf.write_result(res, name, seq_len, result_type="search")
for res in rank_results:
sf.write_result(res, name, seq_len, result_type="ranksearch")
sf.close()
# check results are in files
for f in filelist:
assert os.path.exists(f)
with open(f"{prefix}.contigs.search.csv", "r") as searchres:
this_search_csvset = get_csv_set(searchres)
with open(utils.get_testfile("test-data/test.contigs.search.csv"),
"r") as searchres:
saved_search_csvset = get_csv_set(searchres)
assert saved_search_csvset == this_search_csvset
with open(f"{prefix}.contigs.ranksearch.csv", "r") as searchres:
this_ranksearch_csvset = get_csv_set(searchres)
with open(utils.get_testfile("test-data/test.contigs.ranksearch.csv"),
"r") as searchres:
saved_ranksearch_csvset = get_csv_set(searchres)
assert saved_ranksearch_csvset == this_ranksearch_csvset
def test_gather_guess_tax_at_rank_1():
# one minhash, one set of ranks
hashval = 12345678
ident = 'uniq'
mh1, sig1, lin1 = make_sig_and_lin([hashval], ident, 'a;b;c')
lca_db = LCA_Database(scaled=1, ksize=3)
lca_db.insert(sig1, ident=ident)
lin_db = LineageDB()
lin_db.insert(ident, lin1)
num_hashes = 1
phylum_match_lin = lca_utils.make_lineage('a;b')
gather_results = list(gather_at_rank(mh1, lca_db, lin_db, "class"))
phylum_results = gather_guess_tax_at_rank(gather_results,
num_hashes,
"phylum",
minimum_matches=1)
assert len(phylum_results) == 3
assert phylum_results[0] == phylum_match_lin
assert phylum_results[1] == 1.0
def test_gather_at_rank_3():
# two minhashes, totally distinct ranks
# first sig
hashval1 = 12345678
ident1 = 'first'
mh1, sig1, lin1 = make_sig_and_lin([hashval1], ident1, 'a;b;c')
# second sig
hashval2 = 87654321
ident2 = 'second'
mh2, sig2, lin2 = make_sig_and_lin([hashval2], ident2, 'd;e;f')
# create lca_db w sig1
lca_db = LCA_Database(scaled=1, ksize=3)
lca_db.insert(sig1, ident=ident1)
lca_db.insert(sig2, ident=ident2)
# next, make lin_db
lin_db = LineageDB()
lin_db.insert(ident1, lin1)
lin_db.insert(ident2, lin2)
# search with combined hashvals
search_mh = make_mh([hashval1, hashval2])
gather_results = list(gather_at_rank(search_mh, lca_db, lin_db, "class"))
assert len(gather_results) == 2
assert set([gather_results[0][0],
gather_results[1][0]]) == set([lin1, lin2])
assert set([gather_results[0][1], gather_results[1][1]]) == set([1])
def test_gather_at_rank_2():
#two minhashes, fully shared ranks
# first sig
hashval = 12345678
ident1 = 'first'
mh1, sig1, lin1 = make_sig_and_lin([hashval], ident1, 'a;b;c')
# second sig
hashval2 = 87654321
ident2 = 'second'
mh2, sig2, lin2 = make_sig_and_lin([hashval2], ident2, 'a;b;c')
# create lca_db w sigs
lca_db = LCA_Database(scaled=1, ksize=3)
lca_db.insert(sig1, ident=ident1)
lca_db.insert(sig2, ident=ident2)
# make lin_db
lin_db = LineageDB()
lin_db.insert(ident1, lin1)
lin_db.insert(ident2, lin2)
# search with combined hashvals
search_mh = make_mh([hashval, hashval2])
gather_results = list(gather_at_rank(search_mh, lca_db, lin_db, "class"))
assert len(gather_results) == 1
assert gather_results[0][0] == lin1
assert gather_results[0][1] == 2
def test_gather_at_rank_1():
# one minhash, one set of ranks
hashval = 12345678
ident = 'uniq'
mh1, sig1, lin1 = make_sig_and_lin([hashval], ident, 'a;b;c')
lca_db = LCA_Database(scaled=1, ksize=3)
lca_db.insert(sig1, ident=ident)
lin_db = LineageDB()
lin_db.insert(ident, lin1)
gather_results = list(gather_at_rank(mh1, lca_db, lin_db, "class"))
assert len(gather_results) == 1
assert gather_results[0][0] == lin1
assert gather_results[0][1] == 1
def test_gather_guess_tax_at_each_rank_1():
#two minhashes, fully shared ranks
# first sig
hashval = 12345678
ident1 = 'first'
mh1, sig1, lin1 = make_sig_and_lin([hashval], ident1, 'a;b;c')
# second sig
hashval2 = 87654321
ident2 = 'second'
mh2, sig2, lin2 = make_sig_and_lin([hashval2], ident2, 'a;b;c')
# create lca_db w sigs
lca_db = LCA_Database(scaled=1, ksize=3)
lca_db.insert(sig1, ident=ident1)
lca_db.insert(sig2, ident=ident2)
# make lin_db
lin_db = LineageDB()
lin_db.insert(ident1, lin1)
lin_db.insert(ident2, lin2)
num_hashes = 2
superk_lin = lca_utils.make_lineage('a')
phylum_lin = lca_utils.make_lineage('a;b')
# search with combined hashvals
search_mh = make_mh([hashval, hashval2])
gather_results = list(gather_at_rank(search_mh, lca_db, lin_db, "class"))
rank_results=gather_guess_tax_at_each_rank(gather_results, num_hashes, minimum_matches=1, \
lowest_rank="class",
taxlist=lca_utils.taxlist(include_strain=False))
assert len(rank_results) == 3
assert rank_results[0] == RankSumGatherResult(lineage=superk_lin,
f_ident=1.0,
f_major=1.0)
assert rank_results[1] == RankSumGatherResult(lineage=phylum_lin,
f_ident=1.0,
f_major=1.0)
assert rank_results[2] == RankSumGatherResult(lineage=lin1,
f_ident=1.0,
f_major=1.0)
def test_gather_guess_tax_at_each_rank_3():
# two minhashes, totally distinct ranks
# first sig
hashval1 = 12345678
ident1 = 'first'
mh1, sig1, lin1 = make_sig_and_lin([hashval1], ident1, 'a;b;c')
# second sig
hashval2 = 87654321
ident2 = 'second'
mh2, sig2, lin2 = make_sig_and_lin([hashval2], ident2, 'd;e;f')
# create lca_db w sig1
lca_db = LCA_Database(scaled=1, ksize=3)
lca_db.insert(sig1, ident=ident1)
lca_db.insert(sig2, ident=ident2)
# next, make lin_db
lin_db = LineageDB()
lin_db.insert(ident1, lin1)
lin_db.insert(ident2, lin2)
num_hashes = 2
#winner seems to be def lineage.. will this remain true always?
superk_lin = lca_utils.make_lineage('d')
phylum_lin = lca_utils.make_lineage('d;e')
# search with combined hashvals
search_mh = make_mh([hashval1, hashval2])
gather_results = list(gather_at_rank(search_mh, lca_db, lin_db, "class"))
rank_results=gather_guess_tax_at_each_rank(gather_results, num_hashes, minimum_matches=1, \
lowest_rank="class",
taxlist=lca_utils.taxlist(include_strain=False))
assert len(rank_results) == 3
assert rank_results[0] == RankSumGatherResult(lineage=superk_lin,
f_ident=1.0,
f_major=0.5)
assert rank_results[1] == RankSumGatherResult(lineage=phylum_lin,
f_ident=1.0,
f_major=0.5)
assert rank_results[2] == RankSumGatherResult(lineage=lin2,
f_ident=1.0,
f_major=0.5)
def main(args):
"Main entry point for scripting. Use cmdline for command line entry."
genomebase = os.path.basename(args.genome)
match_rank = 'genus'
# load taxonomy CSV
tax_assign, _ = load_taxonomy_assignments(args.lineages_csv,
start_column=2)
print(f'loaded {len(tax_assign)} tax assignments.')
# load the genome signature
genome_sig = sourmash.load_one_signature(args.genome_sig,
select_moltype=args.alphabet,
ksize=args.ksize)
# load all of the matches from search --containment in the database
with open(args.matches_sig, 'rt') as fp:
try:
siglist = list(
sourmash.load_signatures(fp, do_raise=True, quiet=False))
except sourmash.exceptions.SourmashError:
siglist = []
print(f"loaded {len(siglist)} matches from '{args.matches_sig}'")
# Hack for examining members of our search database: remove exact matches.
new_siglist = []
for ss in siglist:
if genome_sig.similarity(ss) == 1.0:
print(f'removing an identical match: {ss.name()}')
else:
new_siglist.append(ss)
siglist = new_siglist
if not siglist:
# write empty files so snakemake workflows don't complain; exit.
print('no non-identical matches for this genome, exiting.')
if not args.no_search_contigs:
sf = SearchFiles(args.output_prefix,
not args.no_search,
args.gather,
contigs=True)
sf.close()
if args.search_genome:
gf = SearchFiles(args.output_prefix,
not args.no_search,
args.gather,
contigs=False)
gf.close()
return 0
# construct a template minhash object that we can use to create new 'uns
empty_mh = siglist[0].minhash.copy_and_clear()
ksize = empty_mh.ksize
scaled = empty_mh.scaled
moltype = empty_mh.moltype
# create empty LCA database to populate...
lca_db = LCA_Database(ksize=ksize, scaled=scaled, moltype=moltype)
lin_db = LineageDB()
# ...with specific matches.
for ss in siglist:
ident = get_ident(ss)
lineage = tax_assign[ident]
lca_db.insert(ss, ident=ident)
lin_db.insert(ident, lineage)
print(f'loaded {len(siglist)} signatures & created LCA Database')
print('')
print(f'reading contigs from {genomebase}')
screed_iter = screed.open(args.genome)
genome_len = 0
if not args.no_search_contigs:
sf = SearchFiles(args.output_prefix,
not args.no_search,
args.gather,
contigs=True)
for n, record in enumerate(screed_iter):
# look at each contig individually
mh = empty_mh.copy_and_clear()
mh.add_sequence(record.sequence, force=True)
# search, optionally aggregate matched hashes to get containment at rank
seq_len = len(record.sequence)
genome_len += seq_len
num_hashes = len(mh.hashes)
if not args.no_search:
search_results, search_rank_results = search_containment_at_rank(
mh, lca_db, lin_db, match_rank)
if not search_results:
# write to unclassified
sf.unmatched.write(">" + record.name + "\n" +
record.sequence + "\n")
continue # if no search results, don't bother with gather
else:
# first, print normal search --containment results
for sr in search_results:
sf.write_result(sr,
record.name,
seq_len,
result_type="search")
# now, print containment at rank results
for sr in search_rank_results:
sf.write_result(sr,
record.name,
seq_len,
result_type="ranksearch")
if args.gather:
# first, gather at match rank (default genus)
gather_results = list(
gather_at_rank(mh, lca_db, lin_db, match_rank))
# write standard gather_results?
if not gather_results:
# write to unclassified. should only get here if no search OR gather results
sf.unmatched.write(">" + record.name + "\n" +
record.sequence + "\n")
else:
# next, summarize at higher ranks
gather_taxonomy_per_rank = gather_guess_tax_at_each_rank(gather_results, num_hashes, \
minimum_matches=args.gather_min_matches, \
lowest_rank=match_rank, \
taxlist=lca_utils.taxlist(include_strain=False))
#results = list of RankSumGatherResult = namedtuple('RankSumGatherResult', 'lineage, f_ident, f_major')
# write taxonomy out
for gr in gather_taxonomy_per_rank:
sf.write_result(gr,
record.name,
seq_len,
result_type="rankgather")
print(f"Processed {n+1} contigs.")
# close contig files
sf.close()
if args.search_genome:
gf = SearchFiles(args.output_prefix,
not args.no_search,
args.gather,
contigs=False)
# MAG workflow
entire_mh = genome_sig.minhash
genome_name = genome_sig.name()
num_hashes = len(entire_mh.hashes)
if not genome_len:
for record in screed_iter:
genome_len += len(record.sequence)
if not args.no_search:
#results are guaranteed, otherwise would have exited before searching
search_results, search_rank_results = search_containment_at_rank(
entire_mh, lca_db, lin_db, match_rank)
for sr in search_results:
gf.write_result(sr,
genome_name,
genome_len,
result_type="search")
for sr in search_rank_results:
gf.write_result(sr,
genome_name,
genome_len,
result_type="ranksearch")
if args.gather:
gather_results = list(
gather_at_rank(entire_mh, lca_db, lin_db, match_rank))
# next, summarize at higher ranks
gather_taxonomy_per_rank = gather_guess_tax_at_each_rank(gather_results, num_hashes, \
minimum_matches=args.gather_min_matches, \
lowest_rank=match_rank, \
taxlist=lca_utils.taxlist(include_strain=False))
for gather_res in gather_taxonomy_per_rank:
gf.write_result(gather_res,
genome_name,
genome_len,
result_type="rankgather")
# close genome files
gf.close()
return 0