def test_Vsearch_fastas_cmd():
"""Vsearch_fastas instantiates and returns correct form of cmd-line"""
cluster = vsearch.Vsearch_fastas("vsearch")
target = ' '.join([
"vsearch", "--cluster_fast", INFILE_CLUSTER, "--id", THRESHOLD,
"--centroids",
os.path.join(OUTDIR,
PREFIX + THRESHOLD + '.centroids.fasta'), "--msaout",
os.path.join(OUTDIR,
PREFIX + THRESHOLD + '.alignedclusters.fasta'), "--uc",
os.path.join(OUTDIR,
PREFIX + THRESHOLD + '.fast.clusters.uc'), "--consout",
os.path.join(OUTDIR, PREFIX + THRESHOLD + '.consensus_cls_seq.fasta'),
"--db", DB, "--threads", THREADS, "--blast6out",
os.path.join(OUTDIR, PREFIX + THRESHOLD + '.clusterfast.blast6')
])
# fasta_in, outdir, prefix, db, threads, threshold)
assert_equal(
cluster.run(INFILE_CLUSTER,
OUTDIR,
PREFIX,
DB,
THREADS,
THRESHOLD,
dry_run=True), target)
def test_Vsearch_fastas_notexec():
"""Error thrown if vsearch not executable"""
try:
cluster = vsearch.Vsearch_fastas("LICENSE")
except NotExecutableError:
return True
else:
return False
def test_Vsearch_fastas_exec_notexist():
"""Error thrown if Vsearch_fastas executable does not exist"""
try:
cluster = vsearch.Vsearch_fastas(os.path.join(".", "vsearch"))
except NotExecutableError:
return True
else:
return False
def test_vsearch_exec():
"""Run vsearch on test data
TODO: finer option could be passed??
"""
cluster = vsearch.Vsearch_fastas("vsearch")
# results are defined in the class:
# factory class for vsearch class returned values
# Results = namedtuple("Results", "command fastaout " +
# "stdout stderr")
# fasta_in, outdir, prefix, db, threads, threshold=0.99
result2 = cluster.run(INFILE_CLUSTER, OUTDIR, PREFIX, DB, THREADS,
THRESHOLD)
# use the named tuple to get the clustering results file
# compare the blast6 output, convert them to sorted lists first
target_blast = get_sorted_list(TARGET_C_FAST_B6)
result_blast = get_sorted_list(result2.blast6)
assert_equal(result_blast, target_blast)
# UC outfiles
target_uc = get_sorted_list(TARGET_C_FAST_UC)
result_uc = get_sorted_list(result2.uc_clusters)
assert_equal(result_uc, target_uc)
# centroids outfiles
target_cent = get_sorted_fa(TARGET_CENTROIDS)
result_cent = get_sorted_fa(result2.centroids)
assert_equal(target_cent, result_cent)
# TARGET_ALIGNED
target_alig = get_sorted_fa(TARGET_ALIGNED)
result_alig = get_sorted_fa(result2.aligned)
assert_equal(target_alig, result_alig)
# TARGET_CONCENSUS
target_conc = get_sorted_fa(TARGET_CONCENSUS)
result_conc = get_sorted_fa(result2.consensus_cls)
assert_equal(target_conc, result_conc)
def test_Vsearch_fastas():
"""Vsearch_fastas instantiates with cmd-line if cd-hit is in $PATH"""
cluster = vsearch.Vsearch_fastas("vsearch")