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test_lca.py
2629 lines (1924 loc) · 91.3 KB
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test_lca.py
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"""
Tests for the 'sourmash lca' command line and high level API.
"""
import os
import shutil
import csv
import pytest
import glob
import sourmash_tst_utils as utils
import sourmash
from sourmash import load_one_signature, SourmashSignature
from sourmash.search import make_jaccard_search_query
from sourmash.lca import lca_utils
from sourmash.lca.lca_utils import LineagePair
from sourmash.picklist import SignaturePicklist, PickStyle
from sourmash_tst_utils import SourmashCommandFailed
def test_api_create_search():
# create a database and then search for result.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
count = lca_db.insert(ss)
assert count == len(ss.minhash)
results = lca_db.search(ss, threshold=0.0)
print(results)
assert len(results) == 1
(similarity, match, filename) = results[0]
assert match.minhash == ss.minhash
def test_api_find_picklist_select():
# does 'find' respect picklists?
sig47 = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
sig63 = sourmash.load_one_signature(utils.get_test_data('63.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(sig47)
lca_db.insert(sig63)
# construct a picklist...
picklist = SignaturePicklist('md5prefix8')
picklist.init(['09a08691'])
# run a 'find' with sig63, should find 47 and 63 both.
search_obj = make_jaccard_search_query(do_containment=True, threshold=0.0)
results = list(lca_db.find(search_obj, sig63))
print(results)
assert len(results) == 2
# now, select on picklist and do another find...
lca_db = lca_db.select(picklist=picklist)
results = list(lca_db.find(search_obj, sig63))
print(results)
assert len(results) == 1
# and check that it is the expected one!
ss = results[0].signature
assert ss.minhash.ksize == 31
assert ss.md5sum().startswith('09a08691c')
def test_api_find_picklist_select_exclude():
# does 'find' respect picklists?
sig47 = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
sig63 = sourmash.load_one_signature(utils.get_test_data('63.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(sig47)
lca_db.insert(sig63)
# construct a picklist...
picklist = SignaturePicklist('md5prefix8', pickstyle= PickStyle.EXCLUDE)
picklist.init(['09a08691'])
# run a 'find' with sig63, should find 47 and 63 both.
search_obj = make_jaccard_search_query(do_containment=True, threshold=0.0)
results = list(lca_db.find(search_obj, sig63))
print(results)
assert len(results) == 2
# now, select on picklist and do another find...
lca_db = lca_db.select(picklist=picklist)
results = list(lca_db.find(search_obj, sig63))
print(results)
assert len(results) == 1
# and check that it is the expected one!
ss = results[0].signature
assert ss.minhash.ksize == 31
assert ss.md5sum().startswith('38729c637')
def test_api_create_insert():
# test some internal implementation stuff: create & then insert a sig.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss)
ident = ss.name
assert len(lca_db.ident_to_name) == 1
assert ident in lca_db.ident_to_name
assert lca_db.ident_to_name[ident] == ident
assert len(lca_db.ident_to_idx) == 1
assert lca_db.ident_to_idx[ident] == 0
assert len(lca_db.hashval_to_idx) == len(ss.minhash)
assert len(lca_db.idx_to_ident) == 1
assert lca_db.idx_to_ident[0] == ident
set_of_values = set()
for vv in lca_db.hashval_to_idx.values():
set_of_values.update(vv)
assert len(set_of_values) == 1
assert set_of_values == { 0 }
assert not lca_db.idx_to_lid # no lineage added
assert not lca_db.lid_to_lineage # no lineage added
def test_api_create_insert_bad_ksize():
# can we insert a ksize=21 signature into a ksize=31 DB? hopefully not.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=21, scaled=1000)
with pytest.raises(ValueError):
lca_db.insert(ss)
def test_api_create_insert_bad_ident():
# can we insert a signature with no/empty ident?
ss1 = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
ss2 = sourmash.load_one_signature(utils.get_test_data('63.fa.sig'),
ksize=31)
ss1.name = ''
ss1.filename = ''
ss2.name = ''
ss2.filename = ''
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss1)
lca_db.insert(ss2)
# SUCCESS!
# would fail, previously :)
def test_api_create_insert_bad_scaled():
# can we insert a scaled=1000 signature into a scaled=500 DB?
# hopefully not.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
assert ss.minhash.scaled == 1000
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=500)
with pytest.raises(ValueError):
lca_db.insert(ss)
def test_api_create_insert_bad_moltype():
# can we insert a DNAsignature into a protein DB?
# hopefully not.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
assert ss.minhash.moltype == 'DNA'
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=500, moltype='protein')
with pytest.raises(ValueError):
lca_db.insert(ss)
def test_api_create_insert_ident():
# test some internal implementation stuff: signature inserted with
# different ident than name.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss, ident='foo')
ident = 'foo'
assert len(lca_db.ident_to_name) == 1
assert ident in lca_db.ident_to_name
assert lca_db.ident_to_name[ident] == ss.name
assert len(lca_db.ident_to_idx) == 1
assert lca_db.ident_to_idx[ident] == 0
assert len(lca_db.hashval_to_idx) == len(ss.minhash)
assert len(lca_db.idx_to_ident) == 1
assert lca_db.idx_to_ident[0] == ident
set_of_values = set()
for vv in lca_db.hashval_to_idx.values():
set_of_values.update(vv)
assert len(set_of_values) == 1
assert set_of_values == { 0 }
assert not lca_db.idx_to_lid # no lineage added
assert not lca_db.lid_to_lineage # no lineage added
assert not lca_db.lineage_to_lid
assert not lca_db.lid_to_idx
def test_api_create_insert_two():
# check internal details if multiple signatures are inserted.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
ss2 = sourmash.load_one_signature(utils.get_test_data('63.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss, ident='foo')
lca_db.insert(ss2, ident='bar')
ident = 'foo'
ident2 = 'bar'
assert len(lca_db.ident_to_name) == 2
assert ident in lca_db.ident_to_name
assert ident2 in lca_db.ident_to_name
assert lca_db.ident_to_name[ident] == ss.name
assert lca_db.ident_to_name[ident2] == ss2.name
assert len(lca_db.ident_to_idx) == 2
assert lca_db.ident_to_idx[ident] == 0
assert lca_db.ident_to_idx[ident2] == 1
combined_mins = set(ss.minhash.hashes.keys())
combined_mins.update(set(ss2.minhash.hashes.keys()))
assert len(lca_db.hashval_to_idx) == len(combined_mins)
assert len(lca_db.idx_to_ident) == 2
assert lca_db.idx_to_ident[0] == ident
assert lca_db.idx_to_ident[1] == ident2
set_of_values = set()
for vv in lca_db.hashval_to_idx.values():
set_of_values.update(vv)
assert len(set_of_values) == 2
assert set_of_values == { 0, 1 }
assert not lca_db.idx_to_lid # no lineage added
assert not lca_db.lid_to_lineage # no lineage added
assert not lca_db.lineage_to_lid
assert not lca_db.lid_to_idx
def test_api_create_insert_w_lineage():
# test some internal implementation stuff - insert signature w/lineage
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lineage = ((LineagePair('rank1', 'name1'),
LineagePair('rank2', 'name2')))
lca_db.insert(ss, lineage=lineage)
# basic ident stuff
ident = ss.name
assert len(lca_db.ident_to_name) == 1
assert ident in lca_db.ident_to_name
assert lca_db.ident_to_name[ident] == ident
assert len(lca_db.ident_to_idx) == 1
assert lca_db.ident_to_idx[ident] == 0
assert len(lca_db.hashval_to_idx) == len(ss.minhash)
assert len(lca_db.idx_to_ident) == 1
assert lca_db.idx_to_ident[0] == ident
# all hash values added
set_of_values = set()
for vv in lca_db.hashval_to_idx.values():
set_of_values.update(vv)
assert len(set_of_values) == 1
assert set_of_values == { 0 }
# check lineage stuff
assert len(lca_db.idx_to_lid) == 1
assert lca_db.idx_to_lid[0] == 0
assert len(lca_db.lid_to_lineage) == 1
assert lca_db.lid_to_lineage[0] == lineage
assert lca_db.lid_to_idx[0] == { 0 }
assert len(lca_db.lineage_to_lid) == 1
assert lca_db.lineage_to_lid[lineage] == 0
def test_api_create_insert_w_bad_lineage():
# test some internal implementation stuff - insert signature w/bad lineage
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lineage = ([LineagePair('rank1', 'name1'),
LineagePair('rank2', 'name2')],)
with pytest.raises(ValueError):
lca_db.insert(ss, lineage=lineage)
def test_api_create_insert_w_bad_lineage_2():
# test some internal implementation stuff - insert signature w/bad lineage
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lineage = 1 # something non-iterable...
with pytest.raises(ValueError):
lca_db.insert(ss, lineage=lineage)
def test_api_create_gather():
# create a database, and then run gather on it.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss)
results = lca_db.gather(ss, threshold_bp=0)
print(results)
assert len(results) == 1
(similarity, match, filename) = results[0]
assert match.minhash == ss.minhash
def test_api_add_genome_lineage():
# LCA_Databases can store/retrieve arbitrary lineages/taxonomies.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lineage = ((LineagePair('rank1', 'name1'),
(LineagePair('rank2', 'name2'))))
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss, lineage=lineage)
somehash = next(iter(ss.minhash.hashes.keys()))
lineages = lca_db.get_lineage_assignments(somehash)
assert len(lineages) == 1
assert lineage in lineages
def test_api_insert_update():
# check that cached parts of LCA_Database are updated when a new
# signature is inserted.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
ss2 = sourmash.load_one_signature(utils.get_test_data('63.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss)
all_mh = [ x.minhash for x in lca_db.signatures() ]
assert ss.minhash in all_mh
# see decorator @cached_property
assert hasattr(lca_db, '_cache')
assert lca_db._cache
# inserting a signature should delete the cache
lca_db.insert(ss2)
assert not hasattr(lca_db, '_cache')
# check that it's rebuilt etc. etc.
all_mh = [ x.minhash for x in lca_db.signatures() ]
assert ss.minhash in all_mh
assert ss2.minhash in all_mh
def test_api_insert_retrieve_check_name():
# check that signatures retrieved from LCA_Database objects have the
# right name.
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss)
sigs = list(lca_db.signatures())
assert len(sigs) == 1
retrieved_sig = sigs[0]
assert retrieved_sig.name == ss.name
assert retrieved_sig.minhash == ss.minhash
def test_api_create_insert_two_then_scale():
# construct database, THEN downsample
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
ss2 = sourmash.load_one_signature(utils.get_test_data('63.fa.sig'),
ksize=31)
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
lca_db.insert(ss)
lca_db.insert(ss2)
# downsample everything to 5000
lca_db.downsample_scaled(5000)
ss.minhash = ss.minhash.downsample(scaled=5000)
ss2.minhash = ss2.minhash.downsample(scaled=5000)
# & check...
combined_mins = set(ss.minhash.hashes.keys())
combined_mins.update(set(ss2.minhash.hashes.keys()))
assert len(lca_db.hashval_to_idx) == len(combined_mins)
def test_api_create_insert_scale_two():
# downsample while constructing database
ss = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'),
ksize=31)
ss2 = sourmash.load_one_signature(utils.get_test_data('63.fa.sig'),
ksize=31)
# downsample to 5000 while inserting:
lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=5000)
count = lca_db.insert(ss)
assert count == 1037
assert count == len(ss.minhash.downsample(scaled=5000))
lca_db.insert(ss2)
# downsample sigs to 5000
ss.minhash = ss.minhash.downsample(scaled=5000)
ss2.minhash = ss2.minhash.downsample(scaled=5000)
# & check...
combined_mins = set(ss.minhash.hashes.keys())
combined_mins.update(set(ss2.minhash.hashes.keys()))
assert len(lca_db.hashval_to_idx) == len(combined_mins)
def test_load_single_db():
filename = utils.get_test_data('lca/delmont-1.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
print(db)
assert ksize == 31
assert scaled == 10000
def test_load_single_db_empty(runtmp):
# test load_single_database on an empty file; should raise ValueError
empty = runtmp.output('empty.lca.json')
with open(empty, "wt") as fp:
pass
with pytest.raises(ValueError) as exc:
db, ksize, scaled = lca_utils.load_single_database(empty)
assert f"'{empty}' is not an LCA database file." in str(exc.value)
def test_databases():
filename1 = utils.get_test_data('lca/delmont-1.lca.json')
filename2 = utils.get_test_data('lca/delmont-2.lca.json')
dblist, ksize, scaled = lca_utils.load_databases([filename1, filename2])
print(dblist)
assert len(dblist) == 2
assert ksize == 31
assert scaled == 10000
def test_databases_load_fail_on_no_JSON():
filename1 = utils.get_test_data('prot/protein.zip')
with pytest.raises(ValueError) as exc:
dblist, ksize, scaled = lca_utils.load_databases([filename1])
err = str(exc.value)
print(err)
assert f"'{filename1}' is not an LCA database file." in err
def test_databases_load_fail_on_dir():
filename1 = utils.get_test_data('lca')
with pytest.raises(ValueError) as exc:
dblist, ksize, scaled = lca_utils.load_databases([filename1])
err = str(exc.value)
print(err)
assert f"'{filename1}' is not a file and cannot be loaded as an LCA database" in err
assert not 'found 0 matches total;' in err
def test_databases_load_fail_on_not_exist():
filename1 = utils.get_test_data('does-not-exist')
with pytest.raises(ValueError) as exc:
dblist, ksize, scaled = lca_utils.load_databases([filename1])
err = str(exc.value)
print(err)
assert f"'{filename1}' is not a file and cannot be loaded as an LCA database" in err
assert not 'found 0 matches total;' in err
def test_db_repr():
filename = utils.get_test_data('lca/delmont-1.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
assert repr(db) == "LCA_Database('{}')".format(filename)
def test_lca_index_signatures_method():
# test 'signatures' method from base class Index
filename = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
siglist = list(db.signatures())
assert len(siglist) == 2
def test_lca_index_select():
# test 'select' method from Index base class.
filename = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
xx = db.select(ksize=31)
assert xx == db
xx = db.select(moltype='DNA')
assert xx == db
xx = db.select(abund=False)
assert xx == db
with pytest.raises(ValueError):
db.select(ksize=21)
with pytest.raises(ValueError):
db.select(moltype='protein')
with pytest.raises(ValueError):
db.select(abund=True)
def test_lca_index_select_picklist():
# test 'select' method from Index base class with a picklist.
filename = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
# construct a picklist...
picklist = SignaturePicklist('md5prefix8')
picklist.init(['50a92740'])
xx = db.select(picklist=picklist)
assert xx == db
siglist = list(db.signatures())
assert len(siglist) == 1
ss = siglist[0]
assert ss.md5sum().startswith('50a92740')
assert ss.minhash.ksize == 31
def test_lca_index_find_picklist_check_overlap():
# make sure 'find' works for picklists that exclude relevant signatures
# (bug #1638)
query_fn = utils.get_test_data('47.fa.sig')
query_sig = sourmash.load_one_signature(query_fn, ksize=31)
db_fn = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(db_fn)
# construct a picklist...
picklist = SignaturePicklist('ident')
picklist.init(['NC_009665.1'])
xx = db.select(picklist=picklist)
assert xx == db
results = list(db.search(query_sig, threshold=0.1))
assert len(results) == 1
def test_lca_index_select_picklist_exclude():
# test 'select' method from Index base class with a picklist.
filename = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
# construct a picklist...
picklist = SignaturePicklist('md5prefix8', pickstyle=PickStyle.EXCLUDE)
picklist.init(['50a92740'])
xx = db.select(picklist=picklist)
assert xx == db
siglist = list(db.signatures())
assert len(siglist) == 1
ss = siglist[0]
assert ss.md5sum().startswith('e88dc390')
assert ss.minhash.ksize == 31
def test_lca_index_select_picklist_twice():
# test 'select' method from Index base class with a picklist.
filename = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
# construct a picklist...
picklist = SignaturePicklist('md5prefix8')
picklist.init(['50a92740'])
xx = db.select(picklist=picklist)
assert xx == db
with pytest.raises(ValueError) as exc:
xx = db.select(picklist=picklist)
assert "we do not (yet) support multiple picklists for LCA databases" in str(exc)
def test_search_db_scaled_gt_sig_scaled():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
sig = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'))
results = db.search(sig, threshold=.01, ignore_abundance=True)
match_sig = results[0][1]
sig.minhash = sig.minhash.downsample(scaled=10000)
assert sig.minhash == match_sig.minhash
def test_search_db_scaled_lt_sig_scaled():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
sig = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'))
sig.minhash = sig.minhash.downsample(scaled=100000)
results = db.search(sig, threshold=.01, ignore_abundance=True)
print(results)
assert results[0][0] == 1.0
match = results[0][1]
orig_sig = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'))
assert orig_sig.minhash.jaccard(match.minhash, downsample=True) == 1.0
def test_gather_db_scaled_gt_sig_scaled():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
sig = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'))
results = db.gather(sig, threshold=.01, ignore_abundance=True)
match_sig = results[0][1]
sig.minhash = sig.minhash.downsample(scaled=10000)
assert sig.minhash == match_sig.minhash
def test_gather_db_scaled_lt_sig_scaled():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
sig = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'))
sig.minhash = sig.minhash.downsample(scaled=100000)
results = db.gather(sig, threshold=.01, ignore_abundance=True)
match_sig = results[0][1]
match_sig.minhash = match_sig.minhash.downsample(scaled=100000)
assert sig.minhash == match_sig.minhash
def test_db_lineage_to_lid():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
d = db.lineage_to_lid
items = list(d.items())
items.sort()
assert len(items) == 2
print(items)
lin1 = items[0][0][-1]
assert lin1.rank == 'strain'
assert lin1.name == 'Shewanella baltica OS185'
lin1 = items[1][0][-1]
assert lin1.rank == 'strain'
assert lin1.name == 'Shewanella baltica OS223'
def test_db_lid_to_idx():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
d = db.lid_to_idx
items = list(d.items())
items.sort()
assert len(items) == 2
print(items)
assert items == [(32, {32}), (48, {48})]
def test_db_idx_to_ident():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
d = db.idx_to_ident
items = list(d.items())
items.sort()
assert len(items) == 2
print(items)
assert items == [(32, 'NC_009665'), (48, 'NC_011663')]
## command line tests
def test_run_sourmash_lca():
status, out, err = utils.runscript('sourmash', ['lca'], fail_ok=True)
assert status != 0 # no args provided, ok ;)
def test_basic_index(runtmp):
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert os.path.exists(lca_db)
assert 'Building LCA database with ksize=31 scaled=10000 moltype=DNA' in runtmp.last_result.err
assert "** assuming column 'MAGs' is identifiers in spreadsheet" in runtmp.last_result.err
assert "** assuming column 'Domain' is superkingdom in spreadsheet" in runtmp.last_result.err
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in runtmp.last_result.err
def test_basic_index_bad_spreadsheet(runtmp):
taxcsv = utils.get_test_data('lca/bad-spreadsheet.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert os.path.exists(lca_db)
assert "** assuming column 'MAGs' is identifiers in spreadsheet" in runtmp.last_result.err
assert "** assuming column 'Domain' is superkingdom in spreadsheet" in runtmp.last_result.err
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in runtmp.last_result.err
def test_basic_index_broken_spreadsheet(runtmp):
# duplicate identifiers in this spreadsheet
taxcsv = utils.get_test_data('lca/bad-spreadsheet-2.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
with pytest.raises(SourmashCommandFailed):
runtmp.sourmash(*cmd)
assert runtmp.last_result.status != 0
assert "multiple lineages for identifier TARA_ASE_MAG_00031" in runtmp.last_result.err
def test_basic_index_too_many_strains_too_few_species(runtmp):
# explicit test for #841, where 'n_species' wasn't getting counted
# if lineage was at strain level resolution.
taxcsv = utils.get_test_data('lca/podar-lineage.csv')
input_sig = utils.get_test_data('47.fa.sig')
lca_db = runtmp.output('out.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig,
'-C', '3', '--split-identifiers']
runtmp.sourmash(*cmd)
assert not 'error: fewer than 20% of lineages' in runtmp.last_result.err
assert runtmp.last_result.status == 0
def test_basic_index_too_few_species(runtmp):
# spreadsheets with too few species should be flagged, unless -f specified
taxcsv = utils.get_test_data('lca/tully-genome-sigs.classify.csv')
# (these don't really matter, should break on load spreadsheet)
input_sig = utils.get_test_data('47.fa.sig')
lca_db = runtmp.output('out.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig, '-C', '3']
with pytest.raises(SourmashCommandFailed):
runtmp.sourmash(*cmd)
assert not '"ERROR: fewer than 20% of lineages have species-level resolution' in runtmp.last_result.err
assert runtmp.last_result.status != 0
def test_basic_index_require_taxonomy(runtmp):
# no taxonomy in here
taxcsv = utils.get_test_data('lca/bad-spreadsheet-3.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json')
cmd = ['lca', 'index', '--require-taxonomy', taxcsv, lca_db, input_sig]
with pytest.raises(SourmashCommandFailed):
runtmp.sourmash(*cmd)
assert runtmp.last_result.status != 0
assert "ERROR: no hash values found - are there any signatures?" in runtmp.last_result.err
def test_basic_index_column_start(runtmp):
taxcsv = utils.get_test_data('lca/delmont-3.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json')
cmd = ['lca', 'index', '-C', '3', taxcsv, lca_db, input_sig]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert os.path.exists(lca_db)
assert "** assuming column 'MAGs' is identifiers in spreadsheet" in runtmp.last_result.err
assert "** assuming column 'Domain' is superkingdom in spreadsheet" in runtmp.last_result.err
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in runtmp.last_result.err
@utils.in_tempdir
def test_index_empty_sketch_name(c):
# create two signatures with empty 'name' attributes
cmd = ['sketch', 'dna', utils.get_test_data('genome-s12.fa.gz'),
utils.get_test_data('genome-s11.fa.gz')]
c.run_sourmash(*cmd)
sig1 = c.output('genome-s11.fa.gz.sig')
assert os.path.exists(sig1)
sig2 = c.output('genome-s12.fa.gz.sig')
assert os.path.exists(sig2)
# can we insert them both?
taxcsv = utils.get_test_data('lca/delmont-1.csv')
cmd = ['lca', 'index', taxcsv, 'zzz', sig1, sig2]
c.run_sourmash(*cmd)
assert os.path.exists(c.output('zzz.lca.json'))
print(c.last_result.out)
print(c.last_result.err)
assert 'WARNING: no lineage provided for 2 sig' in c.last_result.err
def test_basic_index_and_classify_with_tsv_and_gz(runtmp):
taxcsv = utils.get_test_data('lca/delmont-1.tsv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json.gz')
cmd = ['lca', 'index', '--tabs', '--no-header', taxcsv, lca_db, input_sig]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert os.path.exists(lca_db)
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in runtmp.last_result.err
cmd = ['lca', 'classify', '--db', lca_db, '--query', input_sig]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert 'ID,status,superkingdom,phylum,class,order,family,genus,species' in runtmp.last_result.out
assert 'TARA_ASE_MAG_00031,found,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii' in runtmp.last_result.out
assert 'classified 1 signatures total' in runtmp.last_result.err
assert 'loaded 1 LCA databases' in runtmp.last_result.err
def test_basic_index_and_classify(runtmp):
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert os.path.exists(lca_db)
assert "** assuming column 'MAGs' is identifiers in spreadsheet" in runtmp.last_result.err
assert "** assuming column 'Domain' is superkingdom in spreadsheet" in runtmp.last_result.err
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in runtmp.last_result.err
cmd = ['lca', 'classify', '--db', lca_db, '--query', input_sig]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert 'ID,status,superkingdom,phylum,class,order,family,genus,species' in runtmp.last_result.out
assert 'TARA_ASE_MAG_00031,found,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii' in runtmp.last_result.out
assert 'classified 1 signatures total' in runtmp.last_result.err
assert 'loaded 1 LCA databases' in runtmp.last_result.err
def test_index_traverse(runtmp):
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = runtmp.output('delmont-1.lca.json')
in_dir = runtmp.output('sigs')
os.mkdir(in_dir)
shutil.copyfile(input_sig, os.path.join(in_dir, 'q.sig'))
cmd = ['lca', 'index', taxcsv, lca_db, in_dir]
runtmp.sourmash(*cmd)
print(cmd)
print(runtmp.last_result.out)
print(runtmp.last_result.err)
assert os.path.exists(lca_db)
assert "** assuming column 'MAGs' is identifiers in spreadsheet" in runtmp.last_result.err
assert "** assuming column 'Domain' is superkingdom in spreadsheet" in runtmp.last_result.err
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in runtmp.last_result.err
assert 'WARNING: 1 duplicate signatures.' not in runtmp.last_result.err
@utils.in_tempdir
def test_index_traverse_force(c):
# test the use of --force to load all files, not just .sig
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = c.output('delmont-1.lca.json')
in_dir = c.output('sigs')
os.mkdir(in_dir)
# name signature .txt instead of .sig:
shutil.copyfile(input_sig, os.path.join(in_dir, 'q.txt'))
# use --force
cmd = ['lca', 'index', taxcsv, lca_db, in_dir, '-f']
c.run_sourmash(*cmd)
out = c.last_result.out
err = c.last_result.err
print(out)
print(err)
assert os.path.exists(lca_db)
assert "** assuming column 'MAGs' is identifiers in spreadsheet" in err
assert "** assuming column 'Domain' is superkingdom in spreadsheet" in err
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in err
assert 'WARNING: 1 duplicate signatures.' not in err
@utils.in_tempdir
def test_index_from_file_cmdline_sig(c):
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = c.output('delmont-1.lca.json')
file_list = c.output('sigs.list')
with open(file_list, 'wt') as fp:
print(input_sig, file=fp)