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test_lca.py
2698 lines (1991 loc) · 95.9 KB
/
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
from . import sourmash_tst_utils as utils
import sourmash
from sourmash import load_one_signature, SourmashSignature
from sourmash.lca import lca_utils
from sourmash.lca.lca_utils import LineagePair
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_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_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.get_mins())
combined_mins.update(set(ss2.minhash.get_mins()))
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.get_mins()))
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.get_mins())
combined_mins.update(set(ss2.minhash.get_mins()))
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.get_mins())
combined_mins.update(set(ss2.minhash.get_mins()))
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_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_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
with pytest.raises(ValueError):
db.select(ksize=21)
with pytest.raises(ValueError):
db.select(moltype='protein')
def test_lca_index_find_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)
sig = next(iter(db.signatures()))
with pytest.raises(NotImplementedError) as e:
db.find(None)
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)
with pytest.raises(ValueError) as e:
results = db.search(sig, threshold=.01, ignore_abundance=True)
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():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
assert os.path.exists(lca_db)
assert 'Building LCA database with ksize=31 scaled=10000 moltype=DNA' in err
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
def test_basic_index_bad_spreadsheet():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/bad-spreadsheet.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
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
def test_basic_index_broken_spreadsheet():
# duplicate identifiers in this spreadsheet
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/bad-spreadsheet-2.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
status, out, err = utils.runscript('sourmash', cmd, fail_ok=True)
assert status != 0
assert "multiple lineages for identifier TARA_ASE_MAG_00031" in err
def test_basic_index_too_many_strains_too_few_species():
# explicit test for #841, where 'n_species' wasn't getting counted
# if lineage was at strain level resolution.
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/podar-lineage.csv')
input_sig = utils.get_test_data('47.fa.sig')
lca_db = os.path.join(location, 'out.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig,
'-C', '3', '--split-identifiers']
status, out, err = utils.runscript('sourmash', cmd, fail_ok=True)
assert not 'error: fewer than 20% of lineages' in err
assert status == 0
def test_basic_index_too_few_species():
# spreadsheets with too few species should be flagged, unless -f specified
with utils.TempDirectory() as location:
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 = os.path.join(location, 'out.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig, '-C', '3']
status, out, err = utils.runscript('sourmash', cmd, fail_ok=True)
assert not '"ERROR: fewer than 20% of lineages have species-level resolution' in err
assert status != 0
def test_basic_index_require_taxonomy():
# no taxonomy in here
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/bad-spreadsheet-3.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
cmd = ['lca', 'index', '--require-taxonomy', taxcsv, lca_db, input_sig]
status, out, err = utils.runscript('sourmash', cmd, fail_ok=True)
assert status != 0
assert "ERROR: no hash values found - are there any signatures?" in err
def test_basic_index_column_start():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/delmont-3.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
cmd = ['lca', 'index', '-C', '3', taxcsv, lca_db, input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
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
def test_basic_index_and_classify_with_tsv_and_gz():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/delmont-1.tsv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json.gz')
cmd = ['lca', 'index', '--tabs', '--no-header', taxcsv, lca_db, input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
assert os.path.exists(lca_db)
assert '1 identifiers used out of 1 distinct identifiers in spreadsheet.' in err
cmd = ['lca', 'classify', '--db', lca_db, '--query', input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
assert 'ID,status,superkingdom,phylum,class,order,family,genus,species' in out
assert 'TARA_ASE_MAG_00031,found,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii' in out
assert 'classified 1 signatures total' in err
assert 'loaded 1 LCA databases' in err
def test_basic_index_and_classify():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
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
cmd = ['lca', 'classify', '--db', lca_db, '--query', input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
assert 'ID,status,superkingdom,phylum,class,order,family,genus,species' in out
assert 'TARA_ASE_MAG_00031,found,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii' in out
assert 'classified 1 signatures total' in err
assert 'loaded 1 LCA databases' in err
def test_index_traverse():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/delmont-1.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
in_dir = os.path.join(location, 'sigs')
os.mkdir(in_dir)
shutil.copyfile(input_sig, os.path.join(in_dir, 'q.sig'))
cmd = ['lca', 'index', taxcsv, lca_db, in_dir, '--traverse-directory']
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
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_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, '--traverse-directory',
'-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(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)
cmd = ['lca', 'index', taxcsv, lca_db, input_sig, '--from-file', file_list]
c.run_sourmash(*cmd)
out = c.last_result.out
print(out)
err = c.last_result.err
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.' in err
@utils.in_tempdir
def test_index_fail_on_num(c):
# lca index should yield a decent error message when attempted on 'num'
sigfile = utils.get_test_data('num/63.fa.sig')
taxcsv = utils.get_test_data('lca/podar-lineage.csv')
with pytest.raises(ValueError):
c.run_sourmash('lca', 'index', taxcsv, 'xxx.lca.json', sigfile, '-C', '3')
err = c.last_result.err
print(err)
assert 'ERROR: cannot insert signature ' in err
assert 'ERROR: cannot downsample signature; is it a scaled signature?' in err
def test_index_traverse_real_spreadsheet_no_report():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/tara-delmont-SuppTable3.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig, '-f']
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
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 957 distinct identifiers in spreadsheet.' in err
assert 'WARNING: no signatures for 956 spreadsheet rows.' in err
assert 'WARNING: 105 unused lineages.' in err
assert '(You can use --report to generate a detailed report.)' in err
def test_index_traverse_real_spreadsheet_report():
with utils.TempDirectory() as location:
taxcsv = utils.get_test_data('lca/tara-delmont-SuppTable3.csv')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db = os.path.join(location, 'delmont-1.lca.json')
report_loc = os.path.join(location, 'report.txt')
cmd = ['lca', 'index', taxcsv, lca_db, input_sig, '--report',
report_loc, '-f']
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
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 957 distinct identifiers in spreadsheet.' in err
assert 'WARNING: no signatures for 956 spreadsheet rows.' in err
assert 'WARNING: 105 unused lineages.' in err
assert '(You can use --report to generate a detailed report.)' not in err
assert os.path.exists(report_loc)
def test_single_classify():
with utils.TempDirectory() as location:
db1 = utils.get_test_data('lca/delmont-1.lca.json')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
cmd = ['lca', 'classify', '--db', db1, '--query', input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
assert 'TARA_ASE_MAG_00031,found,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii' in out
assert 'classified 1 signatures total' in err
assert 'loaded 1 LCA databases' in err
def test_single_classify_to_output():
with utils.TempDirectory() as location:
db1 = utils.get_test_data('lca/delmont-1.lca.json')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
cmd = ['lca', 'classify', '--db', db1, '--query', input_sig,
'-o', os.path.join(location, 'outfile.txt')]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
outdata = open(os.path.join(location, 'outfile.txt'), 'rt').read()
assert 'TARA_ASE_MAG_00031,found,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii' in outdata
assert 'classified 1 signatures total' in err
assert 'loaded 1 LCA databases' in err
def test_single_classify_empty():
with utils.TempDirectory() as location:
db1 = utils.get_test_data('lca/both.lca.json')
input_sig = utils.get_test_data('GCF_000005845.2_ASM584v2_genomic.fna.gz.sig')
cmd = ['lca', 'classify', '--db', db1, '--query', input_sig]
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
assert 'data/GCF_000005845.2_ASM584v2_genomic.fna.gz,nomatch,,,,,,,,' in out
assert 'classified 1 signatures total' in err
assert 'loaded 1 LCA databases' in err
def test_single_classify_traverse():
with utils.TempDirectory() as location:
db1 = utils.get_test_data('lca/delmont-1.lca.json')
input_sig = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
in_dir = os.path.join(location, 'sigs')
os.mkdir(in_dir)
shutil.copyfile(input_sig, os.path.join(in_dir, 'q.sig'))
cmd = ['lca', 'classify', '--db', db1, '--query', input_sig,
'--traverse-directory']
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
assert 'TARA_ASE_MAG_00031,found,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii' in out
assert 'classified 1 signatures total' in err
assert 'loaded 1 LCA databases' in err
def test_multi_query_classify_traverse():
with utils.TempDirectory() as location:
# both.lca.json is built from both dir and dir2
db1 = utils.get_test_data('lca/both.lca.json')
dir1 = utils.get_test_data('lca/dir1')
dir2 = utils.get_test_data('lca/dir2')
cmd = ['lca', 'classify', '--db', db1, '--query', dir1, dir2,
'--traverse-directory']
status, out, err = utils.runscript('sourmash', cmd)
print(cmd)
print(out)
print(err)
with open(utils.get_test_data('lca/classify-by-both.csv'), 'rt') as fp:
fp_lines = fp.readlines()
out_lines = out.splitlines()
fp_lines.sort()
out_lines.sort()
assert len(fp_lines) == len(out_lines)
for line1, line2 in zip(fp_lines, out_lines):
assert line1.strip() == line2.strip(), (line1, line2)
@utils.in_tempdir
def test_multi_query_classify_query_from_file(c):
# both.lca.json is built from both dir and dir2
db1 = utils.get_test_data('lca/both.lca.json')
dir1_glob = utils.get_test_data('lca/dir1/*.sig')
dir1_files = glob.glob(dir1_glob)
dir2_glob = utils.get_test_data('lca/dir2/*.sig')
dir2_files = glob.glob(dir2_glob)
file_list = c.output('file.list')
with open(file_list, 'wt') as fp:
print("\n".join(dir1_files), file=fp)
print("\n".join(dir2_files), file=fp)
cmd = ['lca', 'classify', '--db', db1, '--query-from-file', file_list]
c.run_sourmash(*cmd)
out = c.last_result.out
with open(utils.get_test_data('lca/classify-by-both.csv'), 'rt') as fp:
fp_lines = fp.readlines()
out_lines = out.splitlines()
fp_lines.sort()
out_lines.sort()
assert len(fp_lines) == len(out_lines)
for line1, line2 in zip(fp_lines, out_lines):
assert line1.strip() == line2.strip(), (line1, line2)
@utils.in_tempdir
def test_multi_query_classify_query_from_file_and_query(c):
# both.lca.json is built from both dir and dir2
db1 = utils.get_test_data('lca/both.lca.json')
dir1_glob = utils.get_test_data('lca/dir1/*.sig')
dir1_files = glob.glob(dir1_glob)
dir2_glob = utils.get_test_data('lca/dir2/*.sig')
dir2_files = glob.glob(dir2_glob)
file_list = c.output('file.list')
with open(file_list, 'wt') as fp:
print("\n".join(dir1_files[1:]), file=fp) # leave off first one
print("\n".join(dir2_files), file=fp)
cmd = ['lca', 'classify', '--db', db1, '--query', dir1_files[0],
'--query-from-file', file_list]