def test_vsearch_derep_exec():
"""VSEARCH dereplicates test data"""
mode = '--derep_fulllength'
vsearch_exe = vsearch.Vsearch("vsearch")
result = vsearch_exe.run(mode, INFILE_DEREP, OUTFILE_DEREP)
with open(TARGET_DEREP, 'r') as target_fh:
with open(result.outfilename, 'r') as test_fh:
assert_equal(target_fh.read(), test_fh.read())
def test_vsearch_cluster_exec():
"""VSEARCH clusters test data"""
mode = '--usearch_global'
vsearch_exe = vsearch.Vsearch("vsearch")
result = vsearch_exe.run(mode, INFILE_CLUSTER, OUTFILE_CLUSTER_UC,
CLUSTER_PARAMS)
compare_sorted_lines(TARGET_CLUSTER_UC, result.outfile_uc)
compare_sorted_lines(TARGET_CLUSTER_B6, result.outfile_b6)
def test_vsearch_notexec():
"""Error thrown if vsearch not executable"""
try:
vsearch_exe = vsearch.Vsearch("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_vsearch_exec_notexist():
"""error thrown if vsearch executable does not exist"""
try:
vsearch_exe = vsearch.Vsearch(os.path.join(".", "vsearch"))
except NotExecutableError:
return True
else:
return False
def test_vsearch_cluster_exec():
"""VSEARCH cluster_fast clusters test data"""
mode = '--cluster_fast'
vsearch_exe = vsearch.Vsearch("vsearch")
result = vsearch_exe.run(mode, INFILE_CLUSTER, OUTFILE_CLUSTER_FAST_UC,
CLUSTER_FAST_PARAMS)
compare_sorted_lines(TARGET_CLUSTER_FAST_UC, result.outfile_uc)
compare_sorted_lines(TARGET_CLUSTER_FAST_B6, result.outfile_b6)
compare_sorted_fasta(TARGET_CLUSTER_FAST_MSA, result.outfile_msa)
def test_vsearch_derep_cmd():
"""VSEARCH wrapper returns correct dereplication cmd-line"""
mode = '--derep_fulllength'
target = ' '.join([
'vsearch', mode, INFILE_DEREP, '--output', OUTFILE_DEREP, '--sizeout'
])
vsearch_exe = vsearch.Vsearch("vsearch")
result = vsearch_exe.run(mode, INFILE_DEREP, OUTFILE_DEREP, dry_run=True)
assert_equal(result.command, target)
def test_vsearch_cluster_cmd():
"""VSEARCH wrapper returns correct clustering cmd-line"""
mode = '--usearch_global'
target = ' '.join([
'vsearch', mode, INFILE_CLUSTER, '--uc', OUTFILE_CLUSTER_UC, ' '.join([
"{0} {1}".format(k, v) for k, v in sorted(CLUSTER_PARAMS.items())
])
])
vsearch_exe = vsearch.Vsearch("vsearch")
result = vsearch_exe.run(mode,
INFILE_CLUSTER,
OUTFILE_CLUSTER_UC,
CLUSTER_PARAMS,
dry_run=True)
assert_equal(result.command, target)
def test_vsearch_path():
"""vsearch is in $PATH"""
vsearch_exe = vsearch.Vsearch("vsearch")