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test_sourmash_compute.py
872 lines (700 loc) · 35.2 KB
/
test_sourmash_compute.py
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"""
Tests for sourmash compute command-line functionality.
"""
import os
import gzip
import shutil
import screed
import glob
import json
import csv
import pytest
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
from sourmash.command_compute import ComputeParameters
from sourmash.cli.compute import subparser
from sourmash.cli import SourmashParser
from sourmash import signature
from sourmash import VERSION
from sourmash_tst_utils import SourmashCommandFailed
def test_do_sourmash_compute():
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)
sigfile = os.path.join(location, 'short.fa.sig')
assert os.path.exists(sigfile)
sig = next(signature.load_signatures(sigfile))
assert str(sig).endswith('short.fa')
def test_do_sourmash_compute_check_num_bounds_negative(runtmp):
c=runtmp
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
sigfile = c.output('short.fa.sig')
with pytest.raises(SourmashCommandFailed):
c.run_sourmash('compute', '-k', '31', '--num-hashes', '-5', '-o', sigfile, '--merge', '"name"', testdata1, testdata2, testdata3)
assert "ERROR: num value must be positive" in c.last_result.err
def test_do_sourmash_compute_check_num_bounds_less_than_minimum(runtmp):
c=runtmp
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
sigfile = c.output('short.fa.sig')
c.run_sourmash('compute', '-k', '31', '--num-hashes', '25', '-o', sigfile, '--merge', '"name"', testdata1, testdata2, testdata3)
assert "WARNING: num value should be >= 50. Continuing anyway." in c.last_result.err
def test_do_sourmash_compute_check_num_bounds_more_than_maximum(runtmp):
c=runtmp
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
sigfile = c.output('short.fa.sig')
c.run_sourmash('compute', '-k', '31', '--num-hashes', '100000', '-o', sigfile, '--merge', '"name"', testdata1, testdata2, testdata3)
assert "WARNING: num value should be <= 50000. Continuing anyway." in c.last_result.err
@utils.in_tempdir
def test_do_sourmash_compute_outdir(c):
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', testdata1,
'--outdir', c.location])
sigfile = os.path.join(c.location, 'short.fa.sig')
assert os.path.exists(sigfile)
sig = next(signature.load_signatures(sigfile))
assert str(sig).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', '-k', '31', '-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', '-k', '31', '-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))
@utils.in_tempdir
def test_do_sourmash_compute_output_and_name_valid_file(c):
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
sigfile = c.output('short.fa.sig')
c.run_sourmash('compute', '-k', '31', '-o', sigfile, '--merge', '"name"', testdata1, testdata2, testdata3)
assert os.path.exists(sigfile)
assert 'calculated 1 signature for 4 sequences taken from 3 files' in c.last_result.err
# is it valid json?
with open(sigfile, 'r') as f:
data = json.load(f)
assert len(data) == 1
sigfile_merged = c.output('short.all.fa.sig')
c.run_sourmash('compute', '-k', '31', '-o', sigfile_merged, '--merge', '"name"', testdata1, testdata2, testdata3)
with open(sigfile_merged, 'r') as f:
data_merged = json.load(f)
assert data[0]['signatures'][0]['mins'] == data_merged[0]['signatures'][0]['mins']
@utils.in_tempdir
def test_do_sourmash_compute_output_and_name_valid_file_outdir(c):
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(c.location, 'short.fa.sig')
with pytest.raises(SourmashCommandFailed) as exc:
c.run_sourmash('compute', '-k', '31', '-o', sigfile,
'--merge', '"name"',
testdata1, testdata2, testdata3,
'--outdir', c.location)
errmsg = c.last_result.err
assert "ERROR: --output-dir doesn't make sense with -o/--output" in errmsg
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', '-k', '31', '--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', '-k', '31', '--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', '-k', '31', '--name', 'foo',
testdata1, '-o', 'foo2.sig'],
in_directory=location)
sigfile2 = os.path.join(location, 'foo2.sig')
assert os.path.exists(sigfile2)
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', '-k', '31', '--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', '-k', '31', '--merge', 'foo',
testdata1],
in_directory=location,
fail_ok=True)
assert status == -1
status, out, err = utils.runscript('sourmash',
['compute', '-k', '31', '--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', '-k', '31', '--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
assert len(ksizes) == 2
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
assert 7 in ksizes
assert 10 in ksizes
assert len(ksizes) == 4
def test_do_sourmash_compute_multik_with_dayhoff():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--dayhoff', '--no-dna',
testdata1],
in_directory=location)
assert 'Computing only Dayhoff-encoded protein (and not nucleotide) ' \
'signatures.' in err
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 7 in ksizes
assert 10 in ksizes
assert all(x.minhash.dayhoff for x in siglist)
assert len(ksizes) == 2
def test_do_sourmash_compute_multik_with_dayhoff_and_dna():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--dayhoff',
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
assert 7 in ksizes
assert 10 in ksizes
assert sum(x.minhash.moltype == 'DNA' for x in siglist) == 2
assert sum(x.minhash.moltype == 'dayhoff' for x in siglist) == 2
assert len(ksizes) == 4
def test_do_sourmash_compute_multik_with_hp():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--hp', '--no-dna',
testdata1],
in_directory=location)
assert 'Computing only hp-encoded protein (and not nucleotide) ' \
'signatures.' in err
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 7 in ksizes
assert 10 in ksizes
assert all(x.minhash.hp for x in siglist)
assert len(ksizes) == 2
def test_do_sourmash_compute_multik_with_hp_and_dna():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--hp',
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 7 in ksizes
assert 10 in ksizes
assert 21 in ksizes
assert 30 in ksizes
assert len(ksizes) == 4
def test_do_sourmash_compute_multik_with_dayhoff_dna_protein():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--dayhoff', '--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) == 6
ksizes = set([ x.minhash.ksize for x in siglist ])
assert 21 in ksizes
assert 30 in ksizes
assert 7 in ksizes
assert 10 in ksizes
assert sum(x.minhash.moltype == 'DNA' for x in siglist) == 2
assert sum(x.minhash.moltype == 'dayhoff' for x in siglist) == 2
assert sum(x.minhash.moltype == 'protein' for x in siglist) == 2
assert len(ksizes) == 4
def test_do_sourmash_compute_multik_with_dayhoff_hp_dna_protein():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--dayhoff', '--hp', '--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) == 8
ksizes = set([ x.minhash.ksize for x in siglist ])
assert 7 in ksizes
assert 10 in ksizes
assert 21 in ksizes
assert 30 in ksizes
assert sum(x.minhash.moltype == 'DNA' for x in siglist) == 2
assert sum(x.minhash.moltype == 'dayhoff' for x in siglist) == 2
assert sum(x.minhash.moltype == 'hp' for x in siglist) == 2
# 2 = dayhoff, 2 = hp = 4 protein
assert sum(x.minhash.moltype == 'protein' for x in siglist) == 2
assert len(ksizes) == 4
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
@utils.in_tempdir
def test_do_sourmash_compute_multik_only_protein(c):
# check sourmash compute with only protein, no nucl
testdata1 = utils.get_test_data('short.fa')
c.run_sourmash('compute', '-k', '21,30',
'--protein', '--no-dna', testdata1)
outfile = os.path.join(c.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 7 in ksizes
assert 10 in ksizes
assert len(ksizes) == 2
def test_do_sourmash_compute_multik_protein_input_bad_ksize():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short-protein.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '20,32',
'--protein', '--no-dna',
'--input-is-protein',
testdata1],
in_directory=location,
fail_ok=True)
outfile = os.path.join(location, 'short-protein.fa.sig')
assert status != 0
assert 'protein ksizes must be divisible by 3' in err
@utils.in_tempdir
def test_do_sourmash_compute_multik_only_protein_no_rna(c):
# test --no-rna as well (otherwise identical to previous test)
testdata1 = utils.get_test_data('short.fa')
c.run_sourmash('compute', '-k', '21,30',
'--protein', '--no-rna', testdata1)
outfile = os.path.join(c.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 7 in ksizes
assert 10 in ksizes
assert len(ksizes) == 2
def test_do_sourmash_compute_protein_bad_sequences():
"""Proper error handling when Ns in dna sequence"""
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.bad.fa')
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,30',
'--protein', '--no-dna',
testdata1],
in_directory=location)
outfile = os.path.join(location, 'short.bad.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 7 in ksizes
assert 10 in ksizes
assert len(ksizes) == 2
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 7 in ksizes
assert 10 in ksizes
assert len(ksizes) == 2
moltype = set([ x.minhash.moltype == '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
scaled_vals = [ x.minhash.scaled for x in siglist ]
assert len(scaled_vals) == 2
assert set(scaled_vals) == { 1 }
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_bad_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', '-1',
testdata1, '-o', outfile],
in_directory=location,
fail_ok=True)
assert status != 0
assert '--scaled value must be >= 1' in err
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
'--scaled', '1000.5',
testdata1, '-o', outfile],
in_directory=location,
fail_ok=True)
assert status != 0
assert '--scaled value must be integer value' in err
status, out, err = utils.runscript('sourmash',
['compute', '-k', '21,31',
'--scaled', '1e9',
testdata1, '-o', outfile],
in_directory=location)
assert status == 0
assert 'WARNING: scaled value is nonsensical!?' in err
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
@utils.in_tempdir
def test_do_sourmash_check_knowngood_dna_comparisons(c):
# this test checks against a known good signature calculated
# by utils/compute-dna-mh-another-way.py
testdata1 = utils.get_test_data('ecoli.genes.fna')
c.run_sourmash('compute', '-k', '21',
'--singleton', '--dna',
testdata1)
sig1 = c.output('ecoli.genes.fna.sig')
assert os.path.exists(sig1)
x = list(signature.load_signatures(sig1))
sig1, sig2 = sorted(x, key=lambda x: x.name)
print(sig1.name)
print(sig2.name)
knowngood = utils.get_test_data('benchmark.dna.sig')
good = list(signature.load_signatures(knowngood))[0]
assert sig2.similarity(good) == 1.0
@utils.in_tempdir
def test_do_sourmash_check_knowngood_dna_comparisons_use_rna(c):
# check the --rna flag; otherwise identical to previous test.
testdata1 = utils.get_test_data('ecoli.genes.fna')
c.run_sourmash('compute', '-k', '21', '--singleton', '--rna',
testdata1)
sig1 = c.output('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_compute_parameters():
args_list = ["compute", "-k", "21,31", "--singleton", "--protein", "--no-dna", "input_file"]
parser = SourmashParser(prog='sourmash')
subp = parser.add_subparsers(title="instruction", dest="cmd", metavar="cmd")
subparser(subp)
args = parser.parse_args(args_list)
params = ComputeParameters.from_args(args)
assert params.ksizes == [21, 31]
assert params.protein == True
assert params.dna == False
assert params.seed == 42
assert params.dayhoff == False
assert params.hp == False
assert params.num_hashes == 500
assert params.scaled == 0
assert params.track_abundance == False