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test_sourmash_sketch.py
1023 lines (800 loc) · 37.8 KB
/
test_sourmash_sketch.py
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"""
Tests for sourmash sketch command-line functionality.
"""
import os
import gzip
import shutil
import screed
import glob
import json
import csv
import pytest
import screed
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.command_sketch import _signatures_for_sketch_factory
def test_dna_defaults():
factory = _signatures_for_sketch_factory([], 'dna', False)
params_list = list(factory.get_compute_params())
assert len(params_list) == 1
params = params_list[0]
assert params.ksizes == [31]
assert params.num_hashes == 0
assert params.scaled == 1000
assert not params.track_abundance
assert params.seed == 42
assert params.dna
assert not params.dayhoff
assert not params.hp
assert not params.protein
def test_dna_override_1():
factory = _signatures_for_sketch_factory(['k=21,scaled=2000,abund'],
'dna', False)
params_list = list(factory.get_compute_params())
assert len(params_list) == 1
params = params_list[0]
assert params.ksizes == [21]
assert params.num_hashes == 0
assert params.scaled == 2000
assert params.track_abundance
assert params.seed == 42
assert params.dna
assert not params.dayhoff
assert not params.hp
assert not params.protein
def test_dna_override_bad_1():
with pytest.raises(ValueError):
factory = _signatures_for_sketch_factory(['k=21,scaledFOO=2000,abund'],
'dna', False)
def test_dna_override_bad_2():
with pytest.raises(ValueError):
factory = _signatures_for_sketch_factory(['k=21,protein'],
'dna', False)
def test_protein_defaults():
factory = _signatures_for_sketch_factory([], 'protein', True)
params_list = list(factory.get_compute_params())
assert len(params_list) == 1
params = params_list[0]
assert params.ksizes == [30] # x3 for now
assert params.num_hashes == 0
assert params.scaled == 200
assert not params.track_abundance
assert params.seed == 42
assert not params.dna
assert not params.dayhoff
assert not params.hp
assert params.protein
def test_protein_override_bad_2():
with pytest.raises(ValueError):
factory = _signatures_for_sketch_factory(['k=21,dna'],
'protein', False)
def test_protein_override_bad_rust_foo():
# mimic 'sourmash sketch protein -p dna'
factory = _signatures_for_sketch_factory([], 'protein', False)
# reach in and avoid error checking to construct a bad params_list.
factory.params_list = [('dna', {})]
# now, get sigs...
siglist = factory()
assert len(siglist) == 1
sig = siglist[0]
# try adding something
testdata1 = utils.get_test_data('ecoli.faa')
record = next(iter(screed.open(testdata1)))
with pytest.raises(ValueError) as exc:
sig.add_protein(record.sequence)
assert 'Invalid hash function: "dna"' in str(exc)
def test_dayhoff_defaults():
factory = _signatures_for_sketch_factory([], 'dayhoff', True)
params_list = list(factory.get_compute_params())
assert len(params_list) == 1
params = params_list[0]
assert params.ksizes == [48] # x3 for now
assert params.num_hashes == 0
assert params.scaled == 200
assert not params.track_abundance
assert params.seed == 42
assert not params.dna
assert params.dayhoff
assert not params.hp
assert not params.protein
def test_dayhoff_override_bad_2():
with pytest.raises(ValueError):
factory = _signatures_for_sketch_factory(['k=21,dna'],
'dayhoff', False)
def test_hp_defaults():
factory = _signatures_for_sketch_factory([], 'hp', True)
params_list = list(factory.get_compute_params())
assert len(params_list) == 1
params = params_list[0]
assert params.ksizes == [126] # x3 for now
assert params.num_hashes == 0
assert params.scaled == 200
assert not params.track_abundance
assert params.seed == 42
assert not params.dna
assert not params.dayhoff
assert params.hp
assert not params.protein
def test_hp_override_bad_2():
with pytest.raises(ValueError):
factory = _signatures_for_sketch_factory(['k=21,dna'],
'hp', False)
def test_multiple_moltypes():
params_foo = ['k=20,num=500,protein',
'k=19,num=400,dayhoff,abund',
'k=30,scaled=200,hp',
'k=30,scaled=200,seed=58']
factory = _signatures_for_sketch_factory(params_foo, 'protein', True)
params_list = list(factory.get_compute_params())
assert len(params_list) == 4
params = params_list[0]
assert params.ksizes == [60] # x3, for now.
assert params.num_hashes == 500
assert params.scaled == 0
assert not params.track_abundance
assert params.seed == 42
assert not params.dna
assert not params.dayhoff
assert not params.hp
assert params.protein
params = params_list[1]
assert params.ksizes == [57] # x3, for now.
assert params.num_hashes == 400
assert params.scaled == 0
assert params.track_abundance
assert params.seed == 42
assert not params.dna
assert params.dayhoff
assert not params.hp
assert not params.protein
params = params_list[2]
assert params.ksizes == [90] # x3, for now.
assert params.num_hashes == 0
assert params.scaled == 200
assert not params.track_abundance
assert params.seed == 42
assert not params.dna
assert not params.dayhoff
assert params.hp
assert not params.protein
params = params_list[3]
assert params.ksizes == [90] # x3, for now.
assert params.num_hashes == 0
assert params.scaled == 200
assert not params.track_abundance
assert params.seed == 58
assert not params.dna
assert not params.dayhoff
assert not params.hp
assert params.protein
### command line tests
@utils.in_thisdir
def test_do_sourmash_sketchdna_empty(c):
with pytest.raises(ValueError):
c.run_sourmash('sketch', 'dna')
assert 'error: no input filenames provided! nothing to do - exiting.' in c.last_result.err
@utils.in_thisdir
def test_do_sourmash_sketchprotein_empty(c):
with pytest.raises(ValueError):
c.run_sourmash('sketch', 'protein')
assert 'error: no input filenames provided! nothing to do - exiting.' in c.last_result.err
@utils.in_thisdir
def test_do_sourmash_sketchtranslate_empty(c):
with pytest.raises(ValueError):
c.run_sourmash('sketch', 'translate')
assert 'error: no input filenames provided! nothing to do - exiting.' in c.last_result.err
def test_do_sourmash_sketchdna():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', 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_sketchdna_from_file():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
file_list = os.path.join(location, "filelist.txt")
with open(file_list, 'wt') as fp:
print(testdata1, file=fp)
status, out, err = utils.runscript('sourmash',
['sketch', 'dna',
'--from-file', file_list],
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')
@utils.in_tempdir
def test_do_sourmash_sketchdna_noinput(c):
data = ""
cmd = ['sketch', 'dna', '-', '-o', c.output('xxx.sig')]
c.run_sourmash(*cmd, stdin_data=data)
sigfile = c.output('xxx.sig')
assert not os.path.exists(sigfile)
assert 'no sequences found' in c.last_result.err
@utils.in_tempdir
def test_do_sourmash_sketchdna_noinput_singleton(c):
data = ""
cmd = ['sketch', 'dna', '-', '-o', c.output('xxx.sig'), '--singleton']
c.run_sourmash(*cmd, stdin_data=data)
sigfile = c.output('xxx.sig')
assert not os.path.exists(sigfile)
assert 'no sequences found' in c.last_result.err
@utils.in_tempdir
def test_do_sourmash_sketchdna_noinput_merge(c):
data = ""
cmd = ['sketch', 'dna', '-', '-o', c.output('xxx.sig'), '--merge', 'name']
c.run_sourmash(*cmd, stdin_data=data)
sigfile = c.output('xxx.sig')
assert not os.path.exists(sigfile)
assert 'no sequences found' in c.last_result.err
@utils.in_tempdir
def test_do_sourmash_sketchdna_outdir(c):
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', 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_sketchdna_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',
['sketch', 'dna', '-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_sketchdna_output_zipfile():
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')
outfile = os.path.join(location, 'shorts.zip')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '-o', outfile,
testdata1,
testdata2, testdata3],
in_directory=location)
assert os.path.exists(outfile)
assert not out # stdout should be empty
sigs = list(sourmash.load_file_as_signatures(outfile))
assert len(sigs) == 3
def test_do_sourmash_sketchdna_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',
['sketch', 'dna', '-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_sketchdna_output_and_name_valid_file(c):
# test --merge of multiple input files
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('sketch', 'dna', '-p', 'num=500', '-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('sketch', 'dna', '-p', 'num=500', '-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_sketchdna_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(ValueError) as exc:
c.run_sourmash('sketch', 'dna', '-o', sigfile,
'--merge', '"name"',
testdata1, testdata2, testdata3,
'--outdir', c.location)
errmsg = c.last_result.err
assert "ERROR: --outdir doesn't make sense with -o/--output" in errmsg
def test_do_sourmash_sketchdna_singleton():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '--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 str(sig).endswith('shortName')
def test_do_sourmash_sketchdna_name():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '--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',
['sketch', 'dna', '--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_sketchdna_name_fail_no_output():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '--merge', 'foo',
testdata1],
in_directory=location,
fail_ok=True)
assert status == -1
def test_do_sourmash_sketchdna_fail_no_output():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '--merge', 'foo',
testdata1],
in_directory=location,
fail_ok=True)
assert status == -1
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '--name', 'foo',
testdata1],
in_directory=location,
fail_ok=True)
assert status == -1
def test_do_sourmash_sketchdna_name_from_first():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short3.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '--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_sketchdna_multik():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna', '-p', 'k=31,k=21',
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_sketch_dna_override_protein_fail():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'dna',
'-p', 'k=7,num=500,protein',
testdata1],
in_directory=location,
fail_ok=True)
assert status != 0
assert 'Error creating signatures: Incompatible sketch type' in err
def test_do_sketch_protein_override_dna_fail():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'protein',
'-p', 'k=7,num=500,dna',
testdata1],
in_directory=location,
fail_ok=True)
assert status != 0
assert 'Error creating signatures: Incompatible sketch type' in err
def test_do_sketch_translate_multik_with_protein():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'translate',
'-p', 'k=7,k=10,num=500',
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 7 in ksizes
assert 10 in ksizes
def test_do_sketch_translate_multik_with_protein_from_file():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
file_list = os.path.join(location, "filelist.txt")
with open(file_list, 'wt') as fp:
print(testdata1, file=fp)
status, out, err = utils.runscript('sourmash',
['sketch', 'translate',
'-p', 'k=7,k=10,num=500',
'--from-file', file_list],
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 7 in ksizes
assert 10 in ksizes
def test_do_sketch_translate_multik_with_dayhoff():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'translate',
'-p', 'k=7,k=10,num=500',
'--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) == 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)
def test_do_sketch_translate_multik_with_hp():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
status, out, err = utils.runscript('sourmash',
['sketch', 'translate',
'-p', 'k=7,k=10,num=500',
'--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) == 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)
@utils.in_tempdir
def test_do_sourmash_sketch_translate_multik_only_protein(c):
# check sourmash sketch_translate with only protein, no nucl
testdata1 = utils.get_test_data('short.fa')
c.run_sourmash('sketch', 'translate', '-p', 'k=7,k=10,num=500',
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
def test_do_sourmash_sketch_translate_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',
['sketch', 'translate',
'-p', 'k=7,k=10,num=500',
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
def test_do_sketch_protein_multik_input():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('ecoli.faa')
status, out, err = utils.runscript('sourmash',
['sketch', 'protein',
'-p', 'k=7,k=10,num=500',
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
moltype = set([ x.minhash.moltype == 'protein'
for x in siglist ])
assert len(moltype) == 1
assert True in moltype
def test_do_sketch_protein_multik_input_from_file():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('ecoli.faa')
file_list = os.path.join(location, "filelist.txt")
with open(file_list, 'wt') as fp:
print(testdata1, file=fp)
status, out, err = utils.runscript('sourmash',
['sketch', 'protein',
'-p', 'k=7,k=10,num=500',
'--from-file', file_list],
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
moltype = set([ x.minhash.moltype == 'protein'
for x in siglist ])
assert len(moltype) == 1
assert True in moltype
def test_do_sourmash_sketchdna_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',
['sketch', 'dna',
'-p', 'k=21,k=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_sketchdna_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',
['sketch', 'dna',
'-p', 'k=21,k=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_sketchdna_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',
['sketch', 'dna',
'-p', 'k=21,k=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_sketchdna_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',
['sketch', 'dna',
'-p', 'k=21,k=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_sketchdna_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',
['sketch', 'dna',
'-p', 'k=21,k=31,scaled=-1',
testdata1, '-o', outfile],
in_directory=location,
fail_ok=True)
assert status != 0
assert 'scaled is -1, must be >= 1' in err
status, out, err = utils.runscript('sourmash',
['sketch', 'dna',
'-p', 'k=21,k=31,scaled=1000.5',
testdata1, '-o', outfile],
in_directory=location,
fail_ok=True)
assert status != 0
assert "cannot parse scaled='1000.5' as an integer" in err
status, out, err = utils.runscript('sourmash',
['sketch', 'dna',
'-p', 'k=21,k=31,scaled=1000000000',
testdata1, '-o', outfile],
in_directory=location)
assert status == 0
assert 'WARNING: scaled value of 1000000000 is nonsensical!?' in err
def test_do_sketch_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',
['sketch', 'dna',
'-p', 'k=21,k=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',
['sketch', 'protein',
'-p', 'k=7,num=500',
'--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',
['sketch', 'translate',
'-p', 'k=7,num=500',
'--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('sketch', 'dna', '-p', 'k=21,num=500',
'--singleton', 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 ; otherwise identical to previous test.
testdata1 = utils.get_test_data('ecoli.genes.fna')
c.run_sourmash('sketch', 'rna', '-p', 'k=21,num=500', '--singleton',
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',
['sketch', 'protein',
'-p', 'k=7,num=500',
'--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