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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 time
import screed
import time
import glob
import json
from . import sourmash_tst_utils as utils
from sourmash_lib import MinHash
try:
import matplotlib
matplotlib.use('Agg')
except ImportError:
pass
from sourmash_lib import signature
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 "Unrecognized command" in err
def test_do_sourmash_compute():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', testdata1],
in_directory=location)
sigfile = os.path.join(location, 'short.fa.sig')
assert os.path.exists(sigfile)
sig = next(signature.load_signatures(sigfile))
assert sig.name().endswith('short.fa')
def test_do_sourmash_compute_output_valid_file():
""" Trigger bug #123 """
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
sigfile = os.path.join(location, 'short.fa.sig')
status, out, err = utils.runscript('sourmash',
['compute', '-o', sigfile,
testdata1,
testdata2, testdata3],
in_directory=location)
assert os.path.exists(sigfile)
assert not out # stdout should be empty
# is it valid json?
with open(sigfile, 'r') as f:
data = json.load(f)
filesigs = [sig['filename'] for sig in data]
assert all(testdata in filesigs
for testdata in (testdata1, testdata2, testdata3))
def test_do_sourmash_compute_output_stdout_valid():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-o', '-',
testdata1,
testdata2, testdata3],
in_directory=location)
# is it valid json?
data = json.loads(out)
filesigs = [sig['filename'] for sig in data]
assert all(testdata in filesigs
for testdata in (testdata1, testdata2, testdata3))
def test_do_sourmash_compute_output_and_name_valid_file():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
sigfile = os.path.join(location, 'short.fa.sig')
status, out, err = utils.runscript('sourmash',
['compute', '-o', sigfile,
'--merge', '"name"',
testdata1,
testdata2, testdata3],
in_directory=location)
assert os.path.exists(sigfile)
# is it valid json?
import json
with open(sigfile, 'r') as f:
data = json.load(f)
assert len(data) == 1
all_testdata = " ".join([testdata1, testdata2, testdata3])
sigfile_merged = os.path.join(location, 'short.all.fa.sig')
#cmd = "cat {} | {}/sourmash compute -o {} -".format(
cmd = "cat {} | {}/sourmash compute -o {} -".format(
all_testdata, utils.scriptpath(), sigfile_merged)
status, out, err = utils.run_shell_cmd(cmd, in_directory=location)
with open(sigfile_merged, 'r') as f:
data_merged = json.load(f)
assert data[0]['signatures'][0]['mins'] == data_merged[0]['signatures'][0]['mins']
def test_do_sourmash_compute_singleton():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '--singleton',
testdata1],
in_directory=location)
sigfile = os.path.join(location, 'short.fa.sig')
assert os.path.exists(sigfile)
sig = next(signature.load_signatures(sigfile))
assert sig.name().endswith('shortName')
def test_do_sourmash_compute_name():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '--merge', 'foo',
testdata1, '-o', 'foo.sig'],
in_directory=location)
sigfile = os.path.join(location, 'foo.sig')
assert os.path.exists(sigfile)
sig = next(signature.load_signatures(sigfile))
assert sig.name() == 'foo'
status, out, err = utils.runscript('sourmash',
['compute', '--name', 'foo',
testdata1, '-o', 'foo2.sig'],
in_directory=location)
sigfile2 = os.path.join(location, 'foo2.sig')
assert os.path.exists(sigfile)
sig2 = next(signature.load_signatures(sigfile))
assert sig2.name() == 'foo'
assert sig.name() == sig2.name()
def test_do_sourmash_compute_name_fail_no_output():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '--merge', 'foo',
testdata1],
in_directory=location,
fail_ok=True)
assert status == -1
def test_do_sourmash_compute_merge_fail_no_output():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '--merge', 'foo',
testdata1],
in_directory=location,
fail_ok=True)
assert status == -1
status, out, err = utils.runscript('sourmash',
['compute', '--name', 'foo',
testdata1],
in_directory=location,
fail_ok=True)
assert status == -1
def test_do_sourmash_compute_name_from_first():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short3.fa')
status, out, err = utils.runscript('sourmash',
['compute', '--name-from-first',
testdata1],
in_directory=location)
sigfile = os.path.join(location, 'short3.fa.sig')
assert os.path.exists(sigfile)
sig = next(signature.load_signatures(sigfile))
assert sig.name() == 'firstname'
def test_do_sourmash_compute_multik():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
testdata1],
in_directory=location)
outfile = os.path.join(location, 'short.fa.sig')
assert os.path.exists(outfile)
siglist = list(signature.load_signatures(outfile))
assert len(siglist) == 2
ksizes = set([ x.minhash.ksize for x in siglist ])
assert 21 in ksizes
assert 31 in ksizes
def test_do_sourmash_compute_multik_with_protein():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--protein',
testdata1],
in_directory=location)
outfile = os.path.join(location, 'short.fa.sig')
assert os.path.exists(outfile)
with open(outfile, 'rt') as fp:
sigdata = fp.read()
siglist = list(signature.load_signatures(sigdata))
assert len(siglist) == 4
ksizes = set([ x.minhash.ksize for x in siglist ])
assert 21 in ksizes
assert 30 in ksizes
def test_do_sourmash_compute_multik_with_nothing():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
'--no-protein', '--no-dna',
testdata1],
in_directory=location,
fail_ok=True)
outfile = os.path.join(location, 'short.fa.sig')
assert not os.path.exists(outfile)
def test_do_sourmash_compute_multik_protein_bad_ksize():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '20,32',
'--protein', '--no-dna',
testdata1],
in_directory=location,
fail_ok=True)
outfile = os.path.join(location, 'short.fa.sig')
assert not os.path.exists(outfile)
assert 'protein ksizes must be divisible by 3' in err
def test_do_sourmash_compute_multik_only_protein():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--protein', '--no-dna',
testdata1],
in_directory=location)
outfile = os.path.join(location, 'short.fa.sig')
assert os.path.exists(outfile)
with open(outfile, 'rt') as fp:
sigdata = fp.read()
siglist = list(signature.load_signatures(sigdata))
assert len(siglist) == 2
ksizes = set([ x.minhash.ksize for x in siglist ])
assert 21 in ksizes
assert 30 in ksizes
def test_do_sourmash_compute_multik_input_is_protein():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('ecoli.faa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--input-is-protein',
testdata1],
in_directory=location)
outfile = os.path.join(location, 'ecoli.faa.sig')
assert os.path.exists(outfile)
with open(outfile, 'rt') as fp:
sigdata = fp.read()
siglist = list(signature.load_signatures(sigdata))
assert len(siglist) == 2
ksizes = set([ x.minhash.ksize for x in siglist ])
assert 21 in ksizes
assert 30 in ksizes
moltype = set([ x.minhash.is_molecule_type('protein')
for x in siglist ])
assert len(moltype) == 1
assert True in moltype
def test_do_sourmash_compute_multik_outfile():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
outfile = os.path.join(location, 'FOO.xxx')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
testdata1, '-o', outfile],
in_directory=location)
assert os.path.exists(outfile)
siglist = list(signature.load_signatures(outfile))
assert len(siglist) == 2
ksizes = set([ x.minhash.ksize for x in siglist ])
assert 21 in ksizes
assert 31 in ksizes
def test_do_sourmash_compute_with_scaled_1():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
outfile = os.path.join(location, 'FOO.xxx')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
'--scaled', '1',
testdata1, '-o', outfile],
in_directory=location)
assert os.path.exists(outfile)
siglist = list(signature.load_signatures(outfile))
assert len(siglist) == 2
max_hashes = [ x.minhash.max_hash for x in siglist ]
assert len(max_hashes) == 2
assert set(max_hashes) == { 0 }
def test_do_sourmash_compute_with_scaled_2():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
outfile = os.path.join(location, 'FOO.xxx')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
'--scaled', '2',
testdata1, '-o', outfile],
in_directory=location)
assert os.path.exists(outfile)
siglist = list(signature.load_signatures(outfile))
assert len(siglist) == 2
max_hashes = [ x.minhash.max_hash for x in siglist ]
assert len(max_hashes) == 2
assert set(max_hashes) == set([ int(2**64 /2.) ])
def test_do_sourmash_compute_with_scaled():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
outfile = os.path.join(location, 'FOO.xxx')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
'--scaled', '100',
testdata1, '-o', outfile],
in_directory=location)
assert os.path.exists(outfile)
siglist = list(signature.load_signatures(outfile))
assert len(siglist) == 2
max_hashes = [ x.minhash.max_hash for x in siglist ]
assert len(max_hashes) == 2
assert set(max_hashes) == set([ int(2**64 /100.) ])
def test_do_sourmash_compute_with_seed():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
outfile = os.path.join(location, 'FOO.xxx')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
'--seed', '43',
testdata1, '-o', outfile],
in_directory=location)
assert os.path.exists(outfile)
siglist = list(signature.load_signatures(outfile))
assert len(siglist) == 2
seeds = [ x.minhash.seed for x in siglist ]
assert len(seeds) == 2
assert set(seeds) == set([ 43 ])
def test_do_sourmash_check_protein_comparisons():
# this test checks 2 x 2 protein comparisons with E. coli genes.
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('ecoli.faa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21',
'--input-is-protein',
'--singleton',
testdata1],
in_directory=location)
sig1 = os.path.join(location, 'ecoli.faa.sig')
assert os.path.exists(sig1)
testdata2 = utils.get_test_data('ecoli.genes.fna')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21',
'--protein', '--no-dna',
'--singleton',
testdata2],
in_directory=location)
sig2 = os.path.join(location, 'ecoli.genes.fna.sig')
assert os.path.exists(sig2)
# I'm not sure why load_signatures is randomizing order, but ok.
x = list(signature.load_signatures(sig1))
sig1_aa, sig2_aa = sorted(x, key=lambda x: x.name())
x = list(signature.load_signatures(sig2))
sig1_trans, sig2_trans = sorted(x, key=lambda x: x.name())
name1 = sig1_aa.name().split()[0]
assert name1 == 'NP_414543.1'
name2 = sig2_aa.name().split()[0]
assert name2 == 'NP_414544.1'
name3 = sig1_trans.name().split()[0]
assert name3 == 'gi|556503834:2801-3733'
name4 = sig2_trans.name().split()[0]
assert name4 == 'gi|556503834:337-2799'
print(name1, name3, round(sig1_aa.similarity(sig1_trans), 3))
print(name2, name3, round(sig2_aa.similarity(sig1_trans), 3))
print(name1, name4, round(sig1_aa.similarity(sig2_trans), 3))
print(name2, name4, round(sig2_aa.similarity(sig2_trans), 3))
assert round(sig1_aa.similarity(sig1_trans), 3) == 0.0
assert round(sig2_aa.similarity(sig1_trans), 3) == 0.166
assert round(sig1_aa.similarity(sig2_trans), 3) == 0.174
assert round(sig2_aa.similarity(sig2_trans), 3) == 0.0
def test_do_sourmash_check_knowngood_dna_comparisons():
# this test checks against a known good signature calculated
# by utils/compute-dna-mh-another-way.py
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('ecoli.genes.fna')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21',
'--singleton', '--dna',
testdata1],
in_directory=location)
sig1 = os.path.join(location, 'ecoli.genes.fna.sig')
assert os.path.exists(sig1)
x = list(signature.load_signatures(sig1))
sig1, sig2 = sorted(x, key=lambda x: x.name())
knowngood = utils.get_test_data('benchmark.dna.sig')
good = list(signature.load_signatures(knowngood))[0]
assert sig2.similarity(good) == 1.0
def test_do_sourmash_check_knowngood_input_protein_comparisons():
# this test checks against a known good signature calculated
# by utils/compute-input-prot-another-way.py
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('ecoli.faa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21',
'--input-is-protein',
'--singleton',
testdata1],
in_directory=location)
sig1 = os.path.join(location, 'ecoli.faa.sig')
assert os.path.exists(sig1)
x = list(signature.load_signatures(sig1))
sig1_aa, sig2_aa = sorted(x, key=lambda x: x.name())
knowngood = utils.get_test_data('benchmark.input_prot.sig')
good_aa = list(signature.load_signatures(knowngood))[0]
assert sig1_aa.similarity(good_aa) == 1.0
def test_do_sourmash_check_knowngood_protein_comparisons():
# this test checks against a known good signature calculated
# by utils/compute-prot-mh-another-way.py
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('ecoli.genes.fna')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21',
'--singleton', '--protein',
'--no-dna',
testdata1],
in_directory=location)
sig1 = os.path.join(location, 'ecoli.genes.fna.sig')
assert os.path.exists(sig1)
x = list(signature.load_signatures(sig1))
sig1_trans, sig2_trans = sorted(x, key=lambda x: x.name())
knowngood = utils.get_test_data('benchmark.prot.sig')
good_trans = list(signature.load_signatures(knowngood))[0]
assert sig2_trans.similarity(good_trans) == 1.0
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', 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', 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', 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_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', 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 err
assert '0.930' in out
def test_search_gzip():
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', testdata1, testdata2],
in_directory=location)
data = open(os.path.join(location, 'short.fa.sig'), 'rb').read()
with gzip.open(os.path.join(location, 'zzz.gz'), 'wb') as fp:
fp.write(data)
data = open(os.path.join(location, 'short2.fa.sig'), 'rb').read()
with gzip.open(os.path.join(location, 'yyy.gz'), 'wb') as fp:
fp.write(data)
status, out, err = utils.runscript('sourmash',
['search', 'zzz.gz',
'yyy.gz'],
in_directory=location)
print(status, out, err)
assert '1 matches' in err
assert '0.930' in out
def test_search_2():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
status, out, err = utils.runscript('sourmash',
['compute', testdata1, testdata2,
testdata3],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', 'short.fa.sig',
'short2.fa.sig', 'short3.fa.sig'],
in_directory=location)
print(status, out, err)
assert '2 matches' in err
assert '0.930' in out
assert '0.896' in out
def test_search_3():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
status, out, err = utils.runscript('sourmash',
['compute', testdata1, testdata2,
testdata3],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', '-n', '1',
'short.fa.sig',
'short2.fa.sig', 'short3.fa.sig'],
in_directory=location)
print(status, out, err)
assert '2 matches; showing first 1' in err
def test_mash_csv_to_sig():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa.msh.dump')
testdata2 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash', ['import_csv',
testdata1,
'-o', 'xxx.sig'],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31',
'-n', '970', testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['search', '-k', '31',
'short.fa.sig', 'xxx.sig'],
in_directory=location)
print(status, out, err)
assert '1 matches:' in err
assert 'short.fa \t 1.000 \t xxx.sig' in out
def test_do_sourmash_sbt_index_bad_args():
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', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['sbt_index', 'zzz',
'short.fa.sig',
'short2.fa.sig',
'--dna', '--protein'],
in_directory=location, fail_ok=True)
assert "cannot specify both --dna and --protein!" in err
assert status != 0
def test_do_sourmash_sbt_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', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['sbt_index', 'zzz',
'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))
status, out, err = utils.runscript('sourmash',
['sbt_search', 'zzz',
'short.fa.sig'],
in_directory=location)
print(out)
assert testdata1 in out
assert testdata2 in out
def test_do_sourmash_sbt_index_single():
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', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['sbt_index', 'zzz',
'short.fa.sig'],
in_directory=location)
assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))
status, out, err = utils.runscript('sourmash',
['sbt_search', 'zzz',
'short.fa.sig'],
in_directory=location)
print(out)
assert testdata1 in out
def test_do_sourmash_sbt_search_selectprot():
# sbt_index should fail when run on signatures with multiple types
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
args = ['compute', testdata1, testdata2,
'--protein', '--dna', '-k', '30']
status, out, err = utils.runscript('sourmash', args,
in_directory=location)
args = ['sbt_index', 'zzz', 'short.fa.sig', 'short2.fa.sig']
status, out, err = utils.runscript('sourmash', args,
in_directory=location, fail_ok=True)
print(out)
print(err)
assert status != 0
def test_do_sourmash_sbt_search_dnaprotquery():
# sbt_search should fail if non-single query sig given
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
args = ['compute', testdata1, testdata2,
'--protein', '--dna', '-k', '30']
status, out, err = utils.runscript('sourmash', args,
in_directory=location)
args = ['sbt_index', 'zzz', '--protein', 'short.fa.sig',
'short2.fa.sig']
status, out, err = utils.runscript('sourmash', args,
in_directory=location)
assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))
args = ['sbt_search', 'zzz', 'short.fa.sig']
status, out, err = utils.runscript('sourmash', args,
in_directory=location, fail_ok=True)
assert status != 0
print(out)
print(err)
assert 'need exactly one' in err
def test_do_sourmash_sbt_index_traverse():
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', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['sbt_index', 'zzz',
'--traverse-dir', '.'],
in_directory=location)
assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))
assert 'loaded 2 sigs; saving SBT under' in err
status, out, err = utils.runscript('sourmash',
['sbt_search', 'zzz',
'short.fa.sig'],
in_directory=location)
print(out)
assert testdata1 in out
assert testdata2 in out
def test_do_sourmash_sbt_combine():
with utils.TempDirectory() as location:
files = [utils.get_test_data(f) for f in utils.SIG_FILES]
status, out, err = utils.runscript('sourmash',
['sbt_index', 'zzz'] + files,
in_directory=location)
assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))
status, out, err = utils.runscript('sourmash',
['sbt_combine', 'joined',
'zzz.sbt.json', 'zzz.sbt.json'],
in_directory=location)
assert os.path.exists(os.path.join(location, 'joined.sbt.json'))
filename = os.path.splitext(os.path.basename(utils.SIG_FILES[0]))[0]
status, out, err = utils.runscript('sourmash',
['sbt_search', 'zzz'] + [files[0]],
in_directory=location)
print(out)
assert out.count(filename) == 1
status, out, err = utils.runscript('sourmash',
['sbt_search', 'joined'] + [files[0]],
in_directory=location)
print(out)
# TODO: signature is loaded more than once,
# so checking if we get two results.
# If we ever start reporting only one match (even if appears repeated),
# change this test too!
assert out.count(filename) == 2
def test_do_sourmash_sbt_search_otherdir():
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', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['sbt_index', 'xxx/zzz',
'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
assert os.path.exists(os.path.join(location, 'xxx', 'zzz.sbt.json'))
sbt_name = os.path.join(location,'xxx', 'zzz',)
sig_loc = os.path.join(location, 'short.fa.sig')
status, out, err = utils.runscript('sourmash',
['sbt_search', sbt_name, sig_loc])
print(out)
assert testdata1 in out
assert testdata2 in out
def test_do_sourmash_sbt_search_bestonly():
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', testdata1, testdata2],
in_directory=location)
status, out, err = utils.runscript('sourmash',
['sbt_index', 'zzz',
'short.fa.sig',
'short2.fa.sig'],
in_directory=location)
assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))
status, out, err = utils.runscript('sourmash',
['sbt_search', '--best-only', 'zzz',
'short.fa.sig'],
in_directory=location)
print(out)
assert testdata1 in out
def test_compare_with_abundance_1():
with utils.TempDirectory() as location:
# create two signatures
E1 = MinHash(ksize=5, n=5, is_protein=False,
track_abundance=True)
E2 = MinHash(ksize=5, n=5, is_protein=False,
track_abundance=True)
E1.add_sequence('ATGGA')
E2.add_sequence('ATGGA')
s1 = signature.SourmashSignature('', E1, filename='e1', name='e1')
s2 = signature.SourmashSignature('', E2, filename='e2', name='e2')
signature.save_signatures([s1],
open(os.path.join(location, 'e1.sig'), 'w'))
signature.save_signatures([s2],
open(os.path.join(location, 'e2.sig'), 'w'))
status, out, err = utils.runscript('sourmash',
['search', 'e1.sig', 'e2.sig',
'-k' ,'5'],
in_directory=location)
assert '1.000' in out
def test_compare_with_abundance_2():
with utils.TempDirectory() as location:
# create two signatures
E1 = MinHash(ksize=5, n=5, is_protein=False,
track_abundance=True)
E2 = MinHash(ksize=5, n=5, is_protein=False,
track_abundance=True)
E1.add_sequence('ATGGA')
E1.add_sequence('ATGGA')
E2.add_sequence('ATGGA')
s1 = signature.SourmashSignature('', E1, filename='e1', name='e1')
s2 = signature.SourmashSignature('', E2, filename='e2', name='e2')
signature.save_signatures([s1],
open(os.path.join(location, 'e1.sig'), 'w'))
signature.save_signatures([s2],
open(os.path.join(location, 'e2.sig'), 'w'))
status, out, err = utils.runscript('sourmash',
['search', 'e1.sig', 'e2.sig',
'-k' ,'5'],
in_directory=location)
assert '1.0' in out
def test_compare_with_abundance_3():
with utils.TempDirectory() as location:
# create two signatures