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test_sourmash.py
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test_sourmash.py
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"""
Tests for the 'sourmash' command line.
"""
from __future__ import print_function, unicode_literals
import os
import gzip
import shutil
import screed
import glob
import json
import csv
import pytest
import sys
import zipfile
from . import sourmash_tst_utils as utils
import sourmash
from sourmash import MinHash
from sourmash.sbt import SBT, Node
from sourmash.sbtmh import SigLeaf, load_sbt_index
try:
import matplotlib
matplotlib.use('Agg')
except ImportError:
pass
from sourmash import signature
from sourmash import VERSION
def test_run_sourmash():
status, out, err = utils.runscript('sourmash', [], fail_ok=True)
assert status != 0 # no args provided, ok ;)
def test_run_sourmash_badcmd():
status, out, err = utils.runscript('sourmash', ['foobarbaz'], fail_ok=True)
assert status != 0 # bad arg!
assert "cmd: invalid choice" in err
def test_run_sourmash_subcmd_help():
status, out, err = utils.runscript('sourmash', ['sbt'], fail_ok=True)
print(out)
print(err)
assert status != 0 # should fail
assert "invalid choice:" in err
assert "'sbt' (choose from" in err
# should not have printed a Traceback
assert any("Traceback" not in o for o in (err, out))
def test_sourmash_info():
status, out, err = utils.runscript('sourmash', ['info'], fail_ok=False)
# no output to stdout
assert not out
assert "sourmash version" in err
assert "loaded from path" in err
assert VERSION in err
def test_sourmash_info_verbose():
status, out, err = utils.runscript('sourmash', ['info', '-v'])
# no output to stdout
assert not out
assert "khmer version" in err
assert "screed version" in err
assert "loaded from path" in err
@utils.in_tempdir
def test_do_serial_compare(c):
# try doing a compare serial
import numpy
testsigs = utils.get_test_data('genome-s1*.sig')
testsigs = glob.glob(testsigs)
c.run_sourmash('compare', '-o', 'cmp', '-k', '21', '--dna', *testsigs)
cmp_outfile = c.output('cmp')
assert os.path.exists(cmp_outfile)
cmp_out = numpy.load(cmp_outfile)
sigs = []
for fn in testsigs:
sigs.append(sourmash.load_one_signature(fn, ksize=21,
select_moltype='dna'))
cmp_calc = numpy.zeros([len(sigs), len(sigs)])
for i, si in enumerate(sigs):
for j, sj in enumerate(sigs):
cmp_calc[i][j] = si.similarity(sj)
sigs = []
for fn in testsigs:
sigs.append(sourmash.load_one_signature(fn, ksize=21,
select_moltype='dna'))
assert (cmp_out == cmp_calc).all()
@utils.in_tempdir
def test_do_compare_parallel(c):
# try doing a compare parallel
import numpy
testsigs = utils.get_test_data('genome-s1*.sig')
testsigs = glob.glob(testsigs)
c.run_sourmash('compare', '-o', 'cmp', '-k', '21', '--dna',
"--processes", "2", *testsigs)
cmp_outfile = c.output('cmp')
assert os.path.exists(cmp_outfile)
cmp_out = numpy.load(cmp_outfile)
sigs = []
for fn in testsigs:
sigs.append(sourmash.load_one_signature(fn, ksize=21,
select_moltype='dna'))
cmp_calc = numpy.zeros([len(sigs), len(sigs)])
for i, si in enumerate(sigs):
for j, sj in enumerate(sigs):
cmp_calc[i][j] = si.similarity(sj)
sigs = []
for fn in testsigs:
sigs.append(sourmash.load_one_signature(fn, ksize=21,
select_moltype='dna'))
assert (cmp_out == cmp_calc).all()
@utils.in_tempdir
def test_do_basic_compare_using_rna_arg(c):
# try doing a basic compare using --rna instead of --dna
import numpy
testsigs = utils.get_test_data('genome-s1*.sig')
testsigs = glob.glob(testsigs)
c.run_sourmash('compare', '-o', 'cmp', '-k', '21', '--rna', *testsigs)
cmp_outfile = c.output('cmp')
assert os.path.exists(cmp_outfile)
cmp_out = numpy.load(cmp_outfile)
sigs = []
for fn in testsigs:
sigs.append(sourmash.load_one_signature(fn, ksize=21,
select_moltype='dna'))
cmp_calc = numpy.zeros([len(sigs), len(sigs)])
for i, si in enumerate(sigs):
for j, sj in enumerate(sigs):
cmp_calc[i][j] = si.similarity(sj)
assert (cmp_out == cmp_calc).all()
def test_do_compare_quiet():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '--csv', 'xxx',
'-q'],
in_directory=location)
assert not out
assert not err
def test_do_traverse_directory_compare():
with utils.TempDirectory() as location:
status, out, err = utils.runscript('sourmash',
['compare', '--traverse-directory',
'-k 21', '--dna', utils.get_test_data('compare')],
in_directory=location)
print(out)
assert 'genome-s10.fa.gz' in out
assert 'genome-s11.fa.gz' in out
def test_do_compare_output_csv():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '--csv', 'xxx'],
in_directory=location)
with open(os.path.join(location, 'xxx')) as fp:
r = iter(csv.reader(fp))
row = next(r)
print(row)
row = next(r)
print(row)
assert float(row[0]) == 1.0
assert float(row[1]) == 0.93
row = next(r)
assert float(row[0]) == 0.93
assert float(row[1]) == 1.0
# exactly three lines
with pytest.raises(StopIteration) as e:
next(r)
def test_do_compare_downsample():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '--scaled', '200',
'-k', '31', testdata1],
in_directory=location)
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '--scaled', '100',
'-k', '31', testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '--csv', 'xxx'],
in_directory=location)
print(status, out, err)
assert 'downsampling to scaled value of 200' in err
with open(os.path.join(location, 'xxx')) as fp:
lines = fp.readlines()
assert len(lines) == 3
assert lines[1].startswith('1.0,0.6666')
assert lines[2].startswith('0.6666')
def test_do_compare_output_multiple_k():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21', testdata1],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '--csv', 'xxx'],
in_directory=location,
fail_ok=True)
print(status, out, err)
assert status == -1
assert 'multiple k-mer sizes loaded; please specify one' in err
assert '(saw k-mer sizes 21, 31)' in err
def test_do_compare_output_multiple_moltype():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21', '--dna', testdata1],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21', '--protein', testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '--csv', 'xxx'],
in_directory=location,
fail_ok=True)
assert status == -1
assert 'multiple molecule types loaded;' in err
def test_do_compare_dayhoff():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21', '--dayhoff',
'--no-dna', testdata1],
in_directory=location)
assert status == 0
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21', '--dayhoff',
'--no-dna', testdata2],
in_directory=location)
assert status == 0
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '--dayhoff',
'--csv', 'xxx'],
in_directory=location)
true_out = '''[1. 0.94]
[0.94 1. ]
min similarity in matrix: 0.940'''.splitlines()
for line in out:
cleaned_line = line.split('...')[-1].strip()
cleaned_line in true_out
assert status == 0
def test_do_compare_hp():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21', '--hp',
'--no-dna', testdata1],
in_directory=location)
assert status == 0
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21', '--hp',
'--no-dna', testdata2],
in_directory=location)
assert status == 0
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '--hp',
'--csv', 'xxx'],
in_directory=location)
true_out = '''[1. 0.94]
[0.94 1. ]
min similarity in matrix: 0.940'''.splitlines()
for line in out:
cleaned_line = line.split('...')[-1].strip()
cleaned_line in true_out
assert status == 0
@utils.in_tempdir
def test_compare_containment(c):
import numpy
testdata_glob = utils.get_test_data('gather/GCF*.sig')
testdata_sigs = glob.glob(testdata_glob)
c.run_sourmash('compare', '--containment', '-k', '31',
'--csv', 'output.csv', *testdata_sigs)
# load the matrix output of compare --containment
with open(c.output('output.csv'), 'rt') as fp:
r = iter(csv.reader(fp))
headers = next(r)
mat = numpy.zeros((len(headers), len(headers)))
for i, row in enumerate(r):
for j, val in enumerate(row):
mat[i][j] = float(val)
print(mat)
# load in all the input signatures
idx_to_sig = dict()
for idx, filename in enumerate(testdata_sigs):
ss = sourmash.load_one_signature(filename, ksize=31)
idx_to_sig[idx] = ss
# check explicit containment against output of compare
for i in range(len(idx_to_sig)):
ss_i = idx_to_sig[i]
for j in range(len(idx_to_sig)):
ss_j = idx_to_sig[j]
containment = ss_j.contained_by(ss_i)
containment = round(containment, 3)
mat_val = round(mat[i][j], 3)
assert containment == mat_val, (i, j)
@utils.in_tempdir
def test_compare_containment_abund_flatten(c):
s47 = utils.get_test_data('track_abund/47.fa.sig')
s63 = utils.get_test_data('track_abund/63.fa.sig')
c.run_sourmash('compare', '--containment', '-k', '31', s47, s63)
print(c.last_result.out)
print(c.last_result.err)
assert 'NOTE: --containment means signature abundances are flattened' in \
c.last_result.err
@utils.in_tempdir
def test_compare_containment_require_scaled(c):
s47 = utils.get_test_data('num/47.fa.sig')
s63 = utils.get_test_data('num/63.fa.sig')
with pytest.raises(ValueError) as exc:
c.run_sourmash('compare', '--containment', '-k', '31', s47, s63,
fail_ok=True)
assert 'must use scaled signatures with --containment option' in \
c.last_result.err
assert c.last_result.status != 0
def test_do_plot_comparison():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '-o', 'cmp'],
in_directory=location)
status, out, err = utils.runscript('sourmash', ['plot', 'cmp'],
in_directory=location)
assert os.path.exists(os.path.join(location, "cmp.dendro.png"))
assert os.path.exists(os.path.join(location, "cmp.matrix.png"))
def test_do_plot_comparison_2():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '-o', 'cmp'],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['plot', 'cmp', '--pdf'],
in_directory=location)
assert os.path.exists(os.path.join(location, "cmp.dendro.pdf"))
assert os.path.exists(os.path.join(location, "cmp.matrix.pdf"))
def test_do_plot_comparison_3():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '-o', 'cmp'],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['plot', 'cmp', '--labels'],
in_directory=location)
assert os.path.exists(os.path.join(location, "cmp.dendro.png"))
assert os.path.exists(os.path.join(location, "cmp.matrix.png"))
def test_do_plot_comparison_4_output_dir():
with utils.TempDirectory() as location:
output_dir = os.path.join(location, 'xyz_test')
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig', '-o', 'cmp'],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['plot', 'cmp', '--labels',
'--output-dir', output_dir],
in_directory=location)
assert os.path.exists(os.path.join(output_dir, "cmp.dendro.png"))
assert os.path.exists(os.path.join(output_dir, "cmp.matrix.png"))
def test_do_plot_comparison_5_force():
import numpy
with utils.TempDirectory() as location:
D = numpy.zeros([2,2])
D[0, 0] = 5
with open(os.path.join(location, 'cmp'), 'wb') as fp:
numpy.save(fp, D)
with open(os.path.join(location, 'cmp.labels.txt'), 'wt') as fp:
fp.write("a\nb\n")
status, out, err = utils.runscript('sourmash',
['plot', 'cmp', '--labels', '-f'],
in_directory=location)
print(status, out, err)
assert status == 0
def test_do_plot_comparison_4_fail_not_distance():
import numpy
with utils.TempDirectory() as location:
D = numpy.zeros([2,2])
D[0, 0] = 5
with open(os.path.join(location, 'cmp'), 'wb') as fp:
numpy.save(fp, D)
with open(os.path.join(location, 'cmp.labels.txt'), 'wt') as fp:
fp.write("a\nb\n")
status, out, err = utils.runscript('sourmash',
['plot', 'cmp', '--labels'],
in_directory=location, fail_ok=True)
print(status, out, err)
assert status != 0
def test_plot_override_labeltext():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('genome-s10.fa.gz.sig')
testdata2 = utils.get_test_data('genome-s11.fa.gz.sig')
testdata3 = utils.get_test_data('genome-s12.fa.gz.sig')
testdata4 = utils.get_test_data('genome-s10+s11.sig')
inp_sigs = [testdata1, testdata2, testdata3, testdata4]
status, out, err = utils.runscript('sourmash',
['compare'] + inp_sigs + \
['-o', 'cmp', '-k', '21', '--dna'],
in_directory=location)
with open(os.path.join(location, 'new.labels.txt'), 'wt') as fp:
fp.write('a\nb\nc\nd\n')
status, out, err = utils.runscript('sourmash',
['plot', 'cmp',
'--labeltext', 'new.labels.txt'],
in_directory=location)
print(out)
assert 'loading labels from new.labels.txt' in err
expected = """\
0\ta
1\tb
2\tc
3\td"""
assert expected in out
def test_plot_override_labeltext_fail():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('genome-s10.fa.gz.sig')
testdata2 = utils.get_test_data('genome-s11.fa.gz.sig')
testdata3 = utils.get_test_data('genome-s12.fa.gz.sig')
testdata4 = utils.get_test_data('genome-s10+s11.sig')
inp_sigs = [testdata1, testdata2, testdata3, testdata4]
status, out, err = utils.runscript('sourmash',
['compare'] + inp_sigs + \
['-o', 'cmp', '-k', '21', '--dna'],
in_directory=location)
with open(os.path.join(location, 'new.labels.txt'), 'wt') as fp:
fp.write('a\nb\nc\n')
status, out, err = utils.runscript('sourmash',
['plot', 'cmp',
'--labeltext', 'new.labels.txt'],
in_directory=location,
fail_ok=True)
print(out)
print(err)
assert status != 0
assert 'loading labels from new.labels.txt' in err
assert '3 labels != matrix size, exiting' in err
def test_plot_subsample_1():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('genome-s10.fa.gz.sig')
testdata2 = utils.get_test_data('genome-s11.fa.gz.sig')
testdata3 = utils.get_test_data('genome-s12.fa.gz.sig')
testdata4 = utils.get_test_data('genome-s10+s11.sig')
inp_sigs = [testdata1, testdata2, testdata3, testdata4]
status, out, err = utils.runscript('sourmash',
['compare'] + inp_sigs + \
['-o', 'cmp', '-k', '21', '--dna'],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['plot', 'cmp',
'--subsample', '3'],
in_directory=location)
print(out)
expected = """\
0\ts10+s11
1\tgenome-s12.fa.gz
2\tgenome-s10.fa.gz"""
assert expected in out
def test_plot_subsample_2():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('genome-s10.fa.gz.sig')
testdata2 = utils.get_test_data('genome-s11.fa.gz.sig')
testdata3 = utils.get_test_data('genome-s12.fa.gz.sig')
testdata4 = utils.get_test_data('genome-s10+s11.sig')
inp_sigs = [testdata1, testdata2, testdata3, testdata4]
status, out, err = utils.runscript('sourmash',
['compare'] + inp_sigs + \
['-o', 'cmp', '-k', '21', '--dna'],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['plot', 'cmp',
'--subsample', '3',
'--subsample-seed=2'],
in_directory=location)
print(out)
expected = """\
0\tgenome-s12.fa.gz
1\ts10+s11
2\tgenome-s11.fa.gz"""
assert expected in out
def test_search_query_sig_does_not_exist():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short2.fa.sig',
'short.fa.sig'],
in_directory=location, fail_ok=True)
print(status, out, err)
assert status == -1
assert 'Cannot open file' in err
assert len(err.split('\n\r')) < 5
def test_search_subject_sig_does_not_exist():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location, fail_ok=True)
print(status, out, err)
assert status == -1
assert 'Cannot open file' in err
def test_search_second_subject_sig_does_not_exist():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short.fa.sig',
'short.fa.sig', 'short2.fa.sig'],
in_directory=location, fail_ok=True)
print(status, out, err)
assert status == -1
assert 'Cannot open file' in err
def test_search():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status, out, err)
assert '1 matches' in out
assert '93.0%' in out
def test_search_ignore_abundance():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31',
'--track-abundance',
testdata1, testdata2],
in_directory=location)
# Make sure there's different percent matches when using or
# not using abundance
status1, out1, err1 = utils.runscript('sourmash',
['search',
'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status1, out1, err1)
assert '1 matches' in out1
assert '81.5%' in out1
status2, out2, err2 = utils.runscript('sourmash',
['search',
'--ignore-abundance',
'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status2, out2, err2)
assert '1 matches' in out2
assert '93.0%' in out2
# Make sure results are different!
assert out1 != out2
def test_search_csv():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short.fa.sig',
'short2.fa.sig', '-o', 'xxx.csv'],
in_directory=location)
print(status, out, err)
csv_file = os.path.join(location, 'xxx.csv')
with open(csv_file) as fp:
reader = csv.DictReader(fp)
row = next(reader)
assert float(row['similarity']) == 0.93
assert row['name'].endswith('short2.fa')
assert row['filename'].endswith('short2.fa.sig')
assert row['md5'] == '914591cd1130aa915fe0c0c63db8f19d'
@utils.in_tempdir
def test_search_lca_db(c):
# can we do a 'sourmash search' on an LCA database?
query = utils.get_test_data('47.fa.sig')
lca_db = utils.get_test_data('lca/47+63.lca.json')
c.run_sourmash('search', query, lca_db)
print(c)
assert 'NC_009665.1 Shewanella baltica OS185, complete genome' in str(c)
@utils.in_tempdir
def test_gather_lca_db(c):
# can we do a 'sourmash gather' on an LCA database?
query = utils.get_test_data('47+63.fa.sig')
lca_db = utils.get_test_data('lca/47+63.lca.json')
c.run_sourmash('gather', query, lca_db)
print(c)
assert 'NC_009665.1 Shewanella baltica OS185' in str(c.last_result.out)
@utils.in_tempdir
def test_gather_csv_output_filename_bug(c):
# check a bug where the database filename in the output CSV was incorrect
query = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
lca_db_1 = utils.get_test_data('lca/delmont-1.lca.json')
lca_db_2 = utils.get_test_data('lca/delmont-2.lca.json')
c.run_sourmash('gather', query, lca_db_1, lca_db_2, '-o', 'out.csv')
with open(c.output('out.csv'), 'rt') as fp:
r = csv.DictReader(fp)
row = next(r)
assert row['filename'] == lca_db_1
@utils.in_tempdir
def test_compare_no_such_file(c):
with pytest.raises(ValueError) as e:
c.run_sourmash('compare', 'nosuchfile.sig')
assert "file 'nosuchfile.sig' does not exist! exiting." in c.last_result.err
@utils.in_tempdir
def test_compare_no_such_file_force(c):
with pytest.raises(ValueError) as e:
c.run_sourmash('compare', 'nosuchfile.sig', '-f')
print(c.last_result.err)
assert "no signatures found! exiting." in c.last_result.err
def test_compare_no_matching_sigs():
query = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
status, out, err = utils.runscript('sourmash', ['compare', '-k', '100',
query], fail_ok=True)
print(out)
print(err)
assert status
assert 'warning: no signatures loaded at given ksize/molecule type' in err
assert 'no signatures found! exiting.' in err
def test_compare_deduce_molecule():
# deduce DNA vs protein from query, if it is unique
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '30',
'--no-dna', '--protein',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status, out, err)
assert 'min similarity in matrix: 0.91' in out
def test_compare_choose_molecule_dna():
# choose molecule type
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '30',
'--dna', '--protein',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', '--dna', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status, out, err)
assert 'min similarity in matrix: 0.938' in out
def test_compare_choose_molecule_protein():
# choose molecule type
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '30',
'--dna', '--protein',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', '--protein', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status, out, err)
assert 'min similarity in matrix: 0.91' in out
def test_compare_no_choose_molecule_fail():
# choose molecule type
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '30',
'--dna', '--protein',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location,
fail_ok=True)
assert 'multiple molecule types loaded; please specify' in err
assert status != 0
def test_compare_deduce_ksize():
# deduce ksize, if it is unique
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '29',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compare', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status, out, err)
assert 'min similarity in matrix: 0.938' in out
def test_search_deduce_molecule():
# deduce DNA vs protein from query, if it is unique
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '30',
'--no-dna', '--protein',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
print(status, out, err)
assert '1 matches' in out
assert '(k=30, protein)' in err
def test_search_deduce_ksize():
# deduce ksize from query, if it is unique
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '23',
testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short.fa.sig',
'short2.fa.sig'],
in_directory=location)