def run_minowa_predictor_pks_at(pksnames, pksseqs, options):
#Predict PKS AT domain specificities with Minowa et al. method and PKS code (NP searcher / ClustScan / own?)
utils.writefasta(
pksnames, pksseqs, options.raw_predictions_outputfolder + os.sep +
"ctg" + str(options.record_idx) + "_pksseqs.fasta")
#Run PKS signature analysis
logging.info(
"Predicting PKS AT domain substrate specificities by Yadav et al. PKS signature sequences"
)
with TemporaryDirectory(change=True):
PKS_analysis.run_pkssignature_analysis(
path.join(options.raw_predictions_outputfolder,
"ctg" + str(options.record_idx) + "_pksseqs.fasta"),
path.join(options.raw_predictions_outputfolder,
"ctg" + str(options.record_idx) + "_pkssignatures.txt"))
#Minowa method: run Minowa_AT
logging.info(
"Predicting PKS AT domain substrate specificities by Minowa et al. method"
)
with TemporaryDirectory(change=True):
minowa_AT.run_minowa_at(
options.raw_predictions_outputfolder + os.sep + "ctg" +
str(options.record_idx) + "_pksseqs.fasta",
options.raw_predictions_outputfolder + os.sep + "ctg" +
str(options.record_idx) + "_minowa_pkspredoutput.txt")
def test__exit(self):
"Test TemporaryDirectory __exit__() method"
tdir = TemporaryDirectory()
trace = """ Called tempfile.mkdtemp('', 'tmp', None)
Called shutil.rmtree('/fake/tmp/dir')"""
tdir.__exit__(None, None, None)
assert_same_trace(self.tt, trace)
def test__exit(self):
"Test TemporaryDirectory __exit__() method"
tdir = TemporaryDirectory()
trace = """ Called tempfile.mkdtemp('', 'tmp', None)
Called shutil.rmtree('/fake/tmp/dir')"""
tdir.__exit__(None, None, None)
assert_same_trace(self.tt, trace)
def test__enter(self):
"Test TemporaryDirectory __enter__() method"
expected = "/fake/tmp/dir"
trace = """ Called tempfile.mkdtemp('', 'tmp', None)"""
tdir = TemporaryDirectory()
d = tdir.__enter__()
self.assertEqual(d, expected)
self.assertEqual(self.cwd, '/old/cur/dir')
assert_same_trace(self.tt, trace)
def test__enter(self):
"Test TemporaryDirectory __enter__() method"
expected = "/fake/tmp/dir"
trace = """ Called tempfile.mkdtemp('', 'tmp', None)"""
tdir = TemporaryDirectory()
d = tdir.__enter__()
self.assertEqual(d, expected)
self.assertEqual(self.cwd, '/old/cur/dir')
assert_same_trace(self.tt, trace)
def test_change_cwd(self):
"Test TemporaryDirectory changing the cwd"
expected = "/fake/tmp/dir"
trace = """ Called tempfile.mkdtemp('', 'tmp', None)
Called os.getcwd()
Called os.chdir('/fake/tmp/dir')
Called os.chdir('/old/cur/dir')
Called shutil.rmtree('/fake/tmp/dir')"""
tdir = TemporaryDirectory(change=True)
tdir.__enter__()
self.assertEqual(self.cwd, expected)
self.assertEqual(tdir.old_wd, '/old/cur/dir')
tdir.__exit__(None, None, None)
self.assertEqual(self.cwd, '/old/cur/dir')
assert_same_trace(self.tt, trace)
def run_diamond(subcommand: str,
opts: Optional[List[str]] = None) -> RunResult:
""" Run a diamond subcommand, possibly with further options.
Arguments:
subcommand: the diamond subcommand to run
opts: a list of additional argument strings to pass to diamond
Returns:
RunResult of running diamond
"""
config = get_config()
with TemporaryDirectory() as temp_dir:
params = [
config.cb_diamond_executable,
subcommand,
"--threads", str(config.cpus),
"--tmpdir", temp_dir,
]
if opts:
params.extend(opts)
result = execute(params)
if not result.successful():
raise RuntimeError("diamond failed to run: %s -> %s" % (subcommand, result.stderr[-100:]))
return result
def test_minimal(self):
with TemporaryDirectory(change=True) as tempdir:
self.options = build_config(["--minimal", "--output-dir", tempdir],
isolated=True, modules=antismash.get_all_modules())
with patch.object(nrps_pks, "run_on_record", side_effect=RuntimeError("shouldn't run")):
antismash.main.run_antismash(helpers.get_path_to_balhymicin_genbank(),
self.options)
def test_depict_ectoine(self):
with TemporaryDirectory(change=True) as temp:
assert structure_drawer.generate_image(0, "CC1=NCCC(N1)C(=O)O",
temp)
assert os.path.exists("genecluster0.smi")
assert os.path.exists("genecluster0.png")
assert os.path.exists("genecluster0_icon.png")
def generate_trees(smcogs_dir: str, hmm_results: Dict[str, List[HSP]],
genes_within_clusters: List[CDSFeature],
nrpspks_genes: List[CDSFeature]) -> Dict[str, str]:
""" smCOG phylogenetic tree construction """
pks_nrps_gene_names = set(
[feature.get_name() for feature in nrpspks_genes])
logging.info("Calculating and drawing phylogenetic trees of cluster genes "
"with smCOG members")
with TemporaryDirectory(change=True):
cds_features = []
for cds in genes_within_clusters:
gene_id = cds.get_name()
if gene_id not in pks_nrps_gene_names and hmm_results.get(gene_id):
cds_features.append(cds)
args = []
for index, cds in enumerate(cds_features):
smcog = hmm_results[cds.get_name()][0].hit_id.split(":")[0]
args.append([cds, index, smcog, smcogs_dir])
subprocessing.parallel_function(smcog_tree_analysis, args)
files = glob.glob("*.png")
tree_filenames = {}
for filename in files:
tag = filename.rsplit(".png", 1)[0]
tree_filenames[tag] = filename
return tree_filenames
def perform_docking_domain_analysis(options, clusterpksgenes, genecluster,
seq_record, pksnrpsvars):
feature_by_id = utils.get_feature_dict(seq_record)
#log("Predicting PKS gene order by docking domain sequence " \
# "analysis", stdout=True)
startergene, endinggene = find_first_and_last_genes(
clusterpksgenes, pksnrpsvars.domainnamesdict)
with TemporaryDirectory(change=True):
dockinganalysis_dir = utils.get_full_path(__file__, "docking_analysis")
ntermintresdict = extract_nterminus(dockinganalysis_dir,
clusterpksgenes, seq_record,
startergene, feature_by_id)
ctermintresdict = extract_cterminus(dockinganalysis_dir,
clusterpksgenes, seq_record,
endinggene, feature_by_id)
possible_orders = find_possible_orders(clusterpksgenes, startergene,
endinggene)
geneorders, possible_orders_scoredict = rank_biosynthetic_orders(
ntermintresdict, ctermintresdict, startergene, endinggene,
possible_orders)
write_gene_orders_to_html(options, geneorders, possible_orders_scoredict,
genecluster, startergene, endinggene)
#log("Predicting PKS gene order by docking domain sequence " \
# "analysis succeeded.", stdout=True)
#Write html outfile with docking domain analysis output
pksnrpsvars.dockingdomainanalysis.append(genecluster)
return geneorders[0]
def check_diamond_db_compatible(database_file: str) -> bool:
""" Check if the given diamond database is compatible with the installed diamond version.
Arguments:
database_file: the path to the database file to check
Returns:
True if the database file is compatible, False otherwise
"""
with TemporaryDirectory(change=True):
dummy_fasta = "dummy.fa"
dummy_db = "dummy.dmnd"
with open(dummy_fasta, "w") as handle:
handle.write(">test\nM\n")
run_diamond_makedb(dummy_db, dummy_fasta)
compatible_format = _extract_db_format(dummy_db)
try:
db_format = _extract_db_format(database_file)
except ValueError:
return False
if db_format != compatible_format:
logging.debug(
"Incompatible database format for %s. Expected %s but found %s.",
database_file, compatible_format, db_format)
return False
return True
def generate_image(cluster_number: int, smiles: str,
structures_dir: str) -> bool:
""" Constructs an image, if possible, of a cluster's product structure """
filename = "genecluster%d" % cluster_number
png = filename + ".png"
smi = filename + ".smi"
icon = filename + "_icon.png"
with TemporaryDirectory(change=True):
with open(smi, "w") as handler:
handler.write(smiles)
indigo = Indigo()
query = indigo.loadMoleculeFromFile(smi)
renderer = IndigoRenderer(indigo)
# now that the renderer exists, so does the render-coloring option
indigo.setOption("render-coloring", True)
renderer.renderToFile(query, png)
indigo.setOption("render-image-size", 200, 150)
renderer.renderToFile(query, icon)
# was it successful
dircontents = os.listdir(os.getcwd())
# an exception should be raised by indigo, but just in case
if png not in dircontents:
return False
# if so, move the files to the output dir
for filename in [png, icon, smi]:
shutil.copy(filename, structures_dir)
os.remove(filename)
return True
def test_classification_with_colon(self):
# since SMCOG id and description are stored in a string separated by :,
# ensure that descriptions containing : are properly handled
# test gene is AQF52_5530 from CP013129.1
translation = (
"MDTHQREEDPVAARRDRTHYLYLAVIGAVLLGIAVGFLAPGVAVELKPLGTGFVN"
"LIKMMISPIIFCTIVLGVGSVRKAAKVGAVGGLALGYFLVMSTVALAIGLLVGNL"
"LEPGSGLHLTKEIAEAGAKQAEGGGESTPDFLLGIIPTTFVSAFTEGEVLQTLLV"
"ALLAGFALQAMGAAGEPVLRGIGHIQRLVFRILGMIMWVAPVGAFGAIAAVVGAT"
"GAAALKSLAVIMIGFYLTCGLFVFVVLGAVLRLVAGINIWTLLRYLGREFLLILS"
"TSSSESALPRLIAKMEHLGVSKPVVGITVPTGYSFNLDGTAIYLTMASLFVAEAM"
"GDPLSIGEQISLLVFMIIASKGAAGVTGAGLATLAGGLQSHRPELVDGVGLIVGI"
"DRFMSEARALTNFAGNAVATVLVGTWTKEIDKARVTEVLAGNIPFDEKTLVDDHA"
"PVPVPDQRAEGGEEKARAGV")
cds = helpers.DummyCDS(0, len(translation))
cds.translation = translation
results = smcogs.classify.classify_genes([cds])
assert results[cds.get_name(
)][0].hit_id == "SMCOG1212:sodium:dicarboxylate_symporter"
record = helpers.DummyRecord(seq=translation)
record.add_cds_feature(cds)
record.add_cluster(helpers.DummyCluster(0, len(translation)))
with TemporaryDirectory(change=True):
results = smcogs.run_on_record(record, None, self.options)
# if we don't handle multiple semicolons right, this line will crash
results.add_to_record(record)
gene_functions = cds.gene_functions.get_by_tool("smcogs")
assert len(gene_functions) == 1
assert str(gene_functions[0]).startswith(
"transport (smcogs) SMCOG1212:sodium:dicarboxylate_symporter"
" (Score: 416; E-value: 2.3e-126)")
def test_trees(self):
with TemporaryDirectory(change=True):
results = smcogs.run_on_record(self.record, None, self.options)
assert len(results.tree_images) == 7
for image in results.tree_images.values():
assert os.path.exists(
os.path.join(results.relative_tree_path, image))
# test the results function properly
json = results.to_json()
assert smcogs.SMCOGResults.from_json(json,
self.record).to_json() == json
assert smcogs.regenerate_previous_results(
json, self.record, self.options).to_json() == json
for cds in self.record.get_cluster(0).cds_children:
hit = results.best_hits.get(cds.get_name())
if hit:
assert not cds.notes
assert cds.gene_function in [
secmet.feature.GeneFunction.OTHER,
secmet.feature.GeneFunction.CORE
]
results.add_to_record(self.record)
for cds in self.record.get_cluster(0).cds_children:
if cds.sec_met:
continue # no sense checking, because we don't do anything with it
hit = results.best_hits.get(cds.get_name())
if not hit:
assert cds.gene_function == secmet.feature.GeneFunction.OTHER
continue
assert cds.get_name() in results.tree_images
assert len(cds.notes) == 1
assert cds.gene_function != secmet.feature.GeneFunction.OTHER
def run_prodigal(record: Record, options: ConfigType) -> None:
""" Run progidal to annotate prokaryotic sequences
"""
if "basedir" in options.get('prodigal', ''):
basedir = options.prodigal.basedir
else:
basedir = ""
with TemporaryDirectory(change=True):
name = record.id.lstrip('-')
if not name:
name = "unknown"
fasta_file = '%s.fasta' % name
result_file = '%s.predict' % name
with open(fasta_file, 'w') as handle:
seqio.write([record.to_biopython()], handle, 'fasta')
# run prodigal
prodigal = [path.join(basedir, 'prodigal')]
prodigal.extend(['-i', fasta_file, '-f', 'sco', '-o', result_file])
if options.genefinding_tool == "prodigal-m" or len(record.seq) < 20000:
prodigal.extend(['-p', 'meta'])
err = execute(prodigal).stderr
if err.find('Error') > -1:
logging.error("Failed to run prodigal: %r", err)
raise RuntimeError("prodigal error: %s" % err)
found = 0
for line in open(result_file, 'r'):
# skip first line
if not line.startswith('>'):
continue
name, start_chunk, end_chunk, prodigal_strand = line[1:].rstrip(
).split("_")
try:
start = int(start_chunk)
end = int(end_chunk)
if prodigal_strand == "+":
strand = 1
else:
strand = -1
except ValueError:
logging.error('Malformatted prodigal output line %r',
line.rstrip())
continue
if start > end:
strand = -1
start, end = end, start
loc = FeatureLocation(start - 1, end, strand=strand)
translation = record.get_aa_translation_from_location(loc)
feature = CDSFeature(loc,
locus_tag='ctg%s_%s' %
(record.record_index, name),
translation=translation,
translation_table=record.transl_table)
record.add_cds_feature(feature)
found += 1
logging.debug("prodigal found %d CDS features", found)
def test_trees(self):
with TemporaryDirectory(change=True):
# add the classifications to work with
genefunctions.smcogs.classify(self.record.id,
self.record.get_cds_features(),
self.options).add_to_record(
self.record)
results = smcog_trees.run_on_record(self.record, None,
self.options)
assert len(results.tree_images) == 7
for image in results.tree_images.values():
assert os.path.exists(
os.path.join(results.relative_tree_path, image))
# test the results function properly
json = results.to_json()
assert smcog_trees.SMCOGTreeResults.from_json(
json, self.record).to_json() == json
regenerated = smcog_trees.regenerate_previous_results(
json, self.record, self.options)
assert isinstance(regenerated, smcog_trees.SMCOGTreeResults), json
assert regenerated.to_json() == json
results.add_to_record(self.record)
for cds in self.record.get_cds_features():
if cds.gene_functions.get_by_tool("rule-based-clusters"):
continue # no sense checking, because we don't do anything with it
if not cds.gene_functions.get_by_tool("smcogs"):
continue
assert cds.get_name() in results.tree_images
assert len(cds.notes) == 1
assert cds.gene_function != secmet.qualifiers.GeneFunction.OTHER
def test_record_to_json_and_back(self):
filename = get_path_to_nisin_genbank()
records = list(seqio.parse(open(filename), "genbank"))
records = [
Record.from_biopython(rec, taxon="bacteria") for rec in records
]
rec_results = [{}, {}, {}]
results = serialiser.AntismashResults(filename, records, rec_results,
"dummy")
json_handle = StringIO()
results.write_to_file(json_handle)
json_handle.seek(0)
new_results = serialiser.AntismashResults.from_file(json_handle,
taxon="bacteria")
assert results.to_json() == new_results.to_json()
# check no records were lost
assert len(new_results.records) == len(results.records)
# check that the contents of the records is the same
# by converting to biopython and writing to genbanks
original = self.create_data_stream(results.records)
new = self.create_data_stream(new_results.records)
oldvalue = original.getvalue()
newvalue = new.getvalue()
with TemporaryDirectory(change=True):
open("old.json", "w").write(oldvalue)
open("new.json", "w").write(newvalue)
for oldline, newline in zip(oldvalue.split('\n'),
newvalue.split('\n')):
assert oldline == newline
def perform_subclusterblast(options: ConfigType, record: Record, clusters: Dict[str, ReferenceCluster],
proteins: Dict[str, Protein]) -> GeneralResults:
""" Run BLAST on gene cluster proteins of each cluster, parse output and
return result rankings for each cluster
Arguments:
options: antismash Config
record: the Record to analyse
clusters: a dictionary mapping reference cluster name to ReferenceCluster
proteins: a dictionary mapping reference protein name to Protein
Returns:
a GeneralResults instance storing results for all clusters in the
record
"""
results = GeneralResults(record.id, search_type="subclusterblast")
with TemporaryDirectory(change=True):
allcoregenes = get_core_gene_ids(record)
for region in record.get_regions():
# prepare and run diamond
write_fastas_with_all_genes([region], "input.fasta",
partitions=options.cpus)
run_clusterblast_processes(options)
blastoutput = read_clusterblast_output(options)
write_raw_clusterblastoutput(options.output_dir, blastoutput, prefix="subclusterblast")
# parse and score diamond results
_, cluster_names_to_queries = blastparse(blastoutput, record,
min_seq_coverage=40,
min_perc_identity=45)
ranking = score_clusterblast_output(clusters, allcoregenes, cluster_names_to_queries)
logging.debug("Cluster at %s has %d subclusterblast results", region.location, len(ranking))
# store results
region_result = RegionResult(region, ranking, proteins, "subclusterblast")
results.add_region_result(region_result, clusters, proteins)
return results
def internal_homology_blast(record: secmet.Record) -> Dict[int, List[List[str]]]:
""" Run BLAST on gene cluster proteins of each cluster on itself to find
internal homologs
store groups of homologs - including singles - in a dictionary
as a list of lists accordingly
Arguments:
record: the Record to generate groups from
Returns:
a dictionary mapping cluster_number to
a list containing distinct groups represented by
lists of query ids
"""
with TemporaryDirectory(change=True):
logging.info("Finding internal homologs in each gene cluster...")
internalhomologygroups = {}
for cluster in record.get_clusters():
cluster_number = cluster.get_cluster_number()
iquerycluster_names, iqueryclusterseqs = create_blast_inputs(cluster)
query_filename = "internal_input.fasta"
fasta.write_fasta(iquerycluster_names, iqueryclusterseqs, query_filename)
blastoutput = run_internal_blastsearch(query_filename)
queries, _ = blastparse(blastoutput, record, min_seq_coverage=25,
min_perc_identity=30)
groups = find_internal_orthologous_groups(queries, iquerycluster_names)
internalhomologygroups[cluster_number] = groups
return internalhomologygroups
def run_minowa_predictor_pks_cal(pksnrpscoregenes, domaindict, seq_record,
options):
calnames = []
calseqs = []
#Predict PKS CAL domain specificities with Minowa et al. method
logging.info(
"Predicting CAL domain substrate specificities by Minowa et al. method"
)
for feature in pksnrpscoregenes:
locus = utils.get_gene_id(feature)
domaindetails = domaindict[locus]
nr = 0
for tab in domaindetails:
if tab[0] == "CAL_domain":
nr += 1
start = int(tab[1])
end = int(tab[2])
seq = str(utils.get_aa_sequence(feature))[start:end]
name = locus + "_CAL" + str(nr)
calnames.append(name)
calseqs.append(seq)
if len(calnames) > 0:
utils.writefasta(
calnames, calseqs, options.raw_predictions_outputfolder + os.sep +
"ctg" + str(options.record_idx) + "_calseqs.fasta")
with TemporaryDirectory(change=True):
minowa_CAL.run_minowa_cal(
options.raw_predictions_outputfolder + os.sep + "ctg" +
str(options.record_idx) + "_calseqs.fasta",
options.raw_predictions_outputfolder + os.sep + "ctg" +
str(options.record_idx) + "_minowa_calpredoutput.txt")
return calnames, calseqs
def generate_trees(smcogs_dir: str, genes_within_clusters: List[CDSFeature],
nrpspks_genes: List[CDSFeature]) -> Dict[str, str]:
""" smCOG phylogenetic tree construction """
pks_nrps_cds_names = set(feature.get_name() for feature in nrpspks_genes)
logging.info("Calculating and drawing phylogenetic trees of cluster genes "
"with smCOG members")
cds_features = []
for cds in genes_within_clusters:
cds_name = cds.get_name()
if cds_name in pks_nrps_cds_names:
continue
if not cds.gene_functions.get_by_tool("smcogs"):
continue
cds_features.append(cds)
with TemporaryDirectory(change=True):
args = []
for index, cds in enumerate(cds_features):
smcog = cds.gene_functions.get_by_tool("smcogs")[0].description.split(":")[0]
args.append([cds, index, smcog, smcogs_dir])
subprocessing.parallel_function(smcog_tree_analysis, args)
files = glob.glob("*.png")
tree_filenames = {}
for filename in files:
tag = filename.rsplit(".png", 1)[0]
tree_filenames[tag] = filename
return tree_filenames
def run_diamond(query_file: str, database_file: str, mode: str = "blastp",
opts: Optional[List[str]] = None) -> str:
""" Runs diamond, comparing the given query to the given database
Arguments:
query_file: the path of query sequence file
database_file: the path of the database to compare to
mode: the mode to use (defaults to blastp)
opts: any extra options to pass to diamond
Returns:
the output from running diamond
"""
with TemporaryDirectory() as temp_dir:
command = [
"diamond",
mode,
"--db", database_file,
"--threads", str(get_config().cpus),
"--query", query_file,
"--tmpdir", temp_dir,
]
if opts:
command.extend(opts)
result = execute(command)
if not result.successful():
raise RuntimeError("diamond failed to run: %s -> %s" % (command, result.stderr[-100:]))
return result.stdout
def run_kr_stereochemistry_predictions(pksnrpscoregenes, domaindict,
seq_record, options):
#Predict PKS KR domain stereochemistry using pattern as published in ClustScan
krnames = []
krseqs = []
logging.info("Predicting PKS KR activity and stereochemistry using KR " \
"fingerprints from Starcevic et al.")
for feature in pksnrpscoregenes:
locus = utils.get_gene_id(feature)
domaindetails = domaindict[locus]
nr = 0
for tab in domaindetails:
if tab[0] == "PKS_KR":
nr += 1
start = int(tab[1])
end = int(tab[2])
seq = str(utils.get_aa_sequence(feature))[start:end]
name = locus + "_KR" + str(nr)
krnames.append(name)
krseqs.append(seq)
if len(krnames) > 0:
utils.writefasta(
krnames, krseqs, options.raw_predictions_outputfolder + os.sep +
"ctg" + str(options.record_idx) + "_krseqs.fasta")
with TemporaryDirectory(change=True):
kr_analysis.run_kr_analysis(
options.raw_predictions_outputfolder + os.sep + "ctg" +
str(options.record_idx) + "_krseqs.fasta",
options.raw_predictions_outputfolder + os.sep + "ctg" +
str(options.record_idx) + "_krpredoutput.txt")
return krnames, krseqs
def test_minimal(self):
with TemporaryDirectory(change=True) as tempdir:
self.options = build_config(["--minimal", "--output-dir", tempdir],
isolated=True, modules=antismash.get_all_modules())
antismash.main.run_antismash(helpers.get_path_to_balhymicin_genbank(),
self.options)
# make sure it didn't run
minimock.assert_same_trace(self.tracker, "")
def test_bad_partitions(self):
with TemporaryDirectory(change=True):
for i in [-10, -1, 0]:
with self.assertRaisesRegex(ValueError, "Partitions must be greater than 0"):
core.write_fastas_with_all_genes(self.clusters, "test", partitions=i)
for i in ["str", None, 1.5]:
with self.assertRaisesRegex(TypeError, "Partitions must be an int greater than 0"):
core.write_fastas_with_all_genes(self.clusters, "test", partitions=i)
def test_single_partition(self):
self.dummy_cluster.cds_children = [DummyCDS(1, 3)] * 3
with TemporaryDirectory(change=True):
files = core.write_fastas_with_all_genes(self.clusters, "test.fasta", partitions=1)
assert files == ["test.fasta"]
assert os.path.exists("test.fasta")
expected = "".join(">L{0}\nS{0}\n".format(i) for i in range(len(self.clusters)*3))
assert open("test.fasta").read() == expected
def run_and_regenerate_results_for_module(input_file,
module,
options,
expected_record_count=1,
callback=None):
""" Runs antismash end to end over the given file with the given options
and returns the given modules regenerated results
if callback is supplied, it will be called with the output directory path
as an argument before the output directory is cleared
"""
with TemporaryDirectory(change=True) as tempdir:
orig_output = options.output_dir
update_config({"output_dir": tempdir})
json_filename = os.path.join(
options.output_dir,
os.path.basename(input_file).rsplit('.', 1)[0] + ".json")
assert not os.path.exists(json_filename)
try:
antismash.main.run_antismash(input_file, options)
except:
update_config({"output_dir": orig_output})
raise
update_config({"output_dir": orig_output})
results = serialiser.AntismashResults.from_file(
json_filename, options.taxon)
# remove things that were added by results, because otherwise the add isn't tested by detection
# result regeneration
# this should eventually include every feature and qualifier created by antismash
for record in results.records:
record.clear_antismash_domains()
record.clear_cds_motifs()
if callback:
callback(tempdir)
# not the responsibility of modules, but if it's wrong then everything is
assert len(results.results) == expected_record_count
assert len(results.records) == expected_record_count
# ensure all detection stages add their relevant parts
modules_to_regenerate = antismash.main.get_detection_modules()
# don't try and regenerate twice
if not module in modules_to_regenerate:
modules_to_regenerate.append(module)
if expected_record_count == 1:
regenerated = antismash.main.regenerate_results_for_record(
results.records[0], options, modules_to_regenerate,
results.results[0])
final = regenerated[module.__name__]
assert isinstance(final, module_results.ModuleResults)
else:
regenerated = [
antismash.main.regenerate_results_for_record(
record, options, [module], res)
for record, res in zip(results.records, results.results)
]
final = [result[module.__name__] for result in regenerated]
for res in final:
assert isinstance(res, module_results.ModuleResults)
return final
def perform_subclusterblast(options, seq_record, clusters, proteinlocations,
proteinstrands, proteinannotations, proteintags):
#Run BLAST on gene cluster proteins of each cluster and parse output
logging.info("Running NCBI BLAST+ subcluster searches..")
geneclusters = utils.get_sorted_cluster_features(seq_record)
with TemporaryDirectory(change=True):
for genecluster in geneclusters:
clusternumber = utils.get_cluster_number(genecluster)
if options.debug and os.path.exists(options.dbgclusterblast +
os.sep + "subclusterblast" +
os.sep + "cluster" +
str(clusternumber) + ".txt"):
logging.debug(
"Skipping SubClusterblast calculations, using results from %s instead"
% options.dbgclusterblast + os.sep + "subclusterblast" +
os.sep + "cluster" + str(clusternumber) + ".txt")
else:
logging.info(" Gene cluster " + str(clusternumber))
queryclusternames, queryclusterseqs, queryclusterprots = create_blast_inputs(
genecluster, seq_record)
write_clusterblast_inputfiles(options, queryclusternames,
queryclusterseqs)
run_clusterblast_processes(options, searchtype="subclusters")
blastoutput = read_clusterblast_output(options)
write_raw_clusterblastoutput(options.full_outputfolder_path,
blastoutput,
searchtype="subclusters")
logging.info(" Blast search finished. Parsing results...")
minseqcoverage = 40
minpercidentity = 45
blastdict, querylist, hitclusters = parse_blast(
blastoutput, seq_record, minseqcoverage, minpercidentity)
querylist = remove_queries_without_hits(querylist, blastdict)
allcoregenes = [
utils.get_gene_acc(cds)
for cds in utils.get_secmet_cds_features(seq_record)
]
rankedclusters, rankedclustervalues, hitclusterdict, hitclusterdata = score_clusterblast_output(
blastdict, querylist, hitclusters, clusters, allcoregenes)
# store all clusterblast related data in a utils.Storage object and serialize it
subclusterblastStorage = utils.Storage()
subclusterblastStorage.clusternumber = clusternumber
subclusterblastStorage.queryclusterprots = queryclusterprots
subclusterblastStorage.clusters = clusters
subclusterblastStorage.hitclusterdata = hitclusterdata
subclusterblastStorage.rankedclusters = rankedclusters
subclusterblastStorage.rankedclustervalues = rankedclustervalues
subclusterblastStorage.proteintags = proteintags
subclusterblastStorage.proteinlocations = proteinlocations
subclusterblastStorage.proteinannotations = proteinannotations
subclusterblastStorage.proteinstrands = proteinstrands
write_clusterblast_output(options,
seq_record,
subclusterblastStorage,
searchtype="subclusters")
def perform_knownclusterblast(options: ConfigType, record: Record,
reference_clusters: Dict[str, ReferenceCluster],
proteins: Dict[str, Protein]) -> GeneralResults:
""" Run BLAST on gene cluster proteins of each cluster, parse output and
return result rankings for each cluster
Only compares clusters to known clusters from the MIBiG database
Arguments:
options: antismash Config
record: the Record to analyse
clusters: a dictionary mapping reference cluster name to ReferenceCluster
proteins: a dictionary mapping reference protein name to Protein
Returns:
a GeneralResults instance storing results for all clusters in the
record
"""
logging.debug("Running DIAMOND knowncluster searches..")
results = GeneralResults(record.id, search_type="knownclusterblast")
with TemporaryDirectory(change=True) as tempdir:
write_fastas_with_all_genes(record.get_clusters(), "input.fasta")
run_diamond("input.fasta", _get_datafile_path('knownclusterprots'),
tempdir, options)
with open("input.out", 'r') as handle:
blastoutput = handle.read()
write_raw_clusterblastoutput(options.output_dir,
blastoutput,
prefix="knownclusterblast")
clusters_by_number, _ = parse_all_clusters(blastoutput,
record,
min_seq_coverage=40,
min_perc_identity=45)
core_gene_accessions = get_core_gene_ids(record)
for cluster in record.get_clusters():
cluster_number = cluster.get_cluster_number()
cluster_names_to_queries = clusters_by_number.get(cluster_number, {})
ranking = score_clusterblast_output(reference_clusters,
core_gene_accessions,
cluster_names_to_queries)
# store results
cluster_result = ClusterResult(cluster, ranking, proteins,
"knownclusterblast")
results.add_cluster_result(cluster_result, reference_clusters,
proteins)
write_clusterblast_output(options,
record,
cluster_result,
proteins,
searchtype="knownclusterblast")
results.mibig_entries = mibig_protein_homology(blastoutput, record,
reference_clusters)
return results
def test_single_file(self):
self.add_cdses_to_region([DummyCDS(1, i) for i in range(3, 6)])
with TemporaryDirectory(change=True):
files = core.write_fastas_with_all_genes(self.regions,
"test.fasta")
assert files == ["test.fasta"]
assert os.path.exists("test.fasta")
expected = "".join(">L{0}\nS{0}\n".format(i)
for i in range(len(self.regions) * 3))
assert open("test.fasta").read() == expected
def test_classifier(self):
expected = open(path.get_full_path(__file__, "data",
"nisin.txt")).readlines()
with TemporaryDirectory(change=True):
results = smcogs.run_on_record(self.record, None, self.options)
contents = open("smcogs/smcogs.txt").readlines()
assert contents == expected
json = results.to_json()
assert smcogs.SMCOGResults.from_json(json,
self.record).to_json() == json
def run_antismash(self, filename, expected):
with TemporaryDirectory() as output_dir:
update_config({"output_dir": output_dir})
results = helpers.run_and_regenerate_results_for_module(filename, clusterblast, self.options)
update_config({"output_dir": ""})
results, global_results = self.get_results(results)
assert len(results.region_results) == 1
cluster = results.region_results[0]
assert len(cluster.ranking) == expected # will change if database does
self.check_svgs(global_results, expected, output_dir)
return results