def test_write_to_read_from_stream(self):
reader0 = parser.Reader(SAMPLE_FILE)
aavf_obj = reader0.read_records()
out = StringIO()
writer = parser.Writer(out, aavf_obj)
for record in aavf_obj:
writer.write_record(record)
out.seek(0)
aavf = parser.Reader(out).read_records()
out.close()
record_list = [record for record in aavf]
assert isinstance(aavf, AAVF)
assert aavf.metadata.get("fileformat") == "AAVFv1.0", \
"fileformat should be AAVFv1.0, metadata is %s" % aavf.metadata
assert aavf.metadata.get("fileDate") == "20180501", \
"filedate should be 20180501, metadata is %s" % aavf.metadata
assert aavf.metadata.get("source") == "myProgramV1.0", \
"source should be myProgramV1.0, metadata is %s" % aavf.metadata
assert aavf.metadata.get("reference") == ["hxb2.fas"], \
"reference list should be [hxb2.fas], metadata is %s" % aavf.metadata
assert aavf.infos
assert aavf.filters
assert len(record_list) == 7
# all data lines should be the same as in the sample file
for record in record_list:
assert isinstance(record, Record)
def test_write_and_format_decimals(self):
"""Test whether writes to file work with specifying a certain number
of decimals for the ALT_FREQ field output as expected."""
for num_dec in range(3, 6):
reader = parser.Reader(SAMPLE_FILE)
aavf_obj = reader.read_records()
out = fhandle('sampleoutput4.aavf', "w+")
writer = parser.Writer(out, aavf_obj)
records = list(aavf_obj)
for record in records:
writer.write_record(record, decimals=num_dec)
out.close()
reader1 = parser.Reader(TEST_PATH +
'/sampleoutput4.aavf').read_records()
reader2 = parser.Reader(SAMPLE_FILE).read_records()
writer.close()
# each ALT_FREQ field's string should have num_dec + 2 characters
# e.g. 0.123 if num_dec is three
for left, right in zip(reader1, reader2):
assert left.INFO == right.INFO
assert left.ALT_FREQ == round(right.ALT_FREQ, num_dec), \
"%s and %s should be the same up to the %dth decimal place" % (left.ALT_FREQ, right.ALT_FREQ, num_dec)
def test_write(self):
"""Test whether the INFO section can be written correctly."""
reader = parser.Reader(SAMPLE_FILE)
aavf_obj = reader.read_records()
out = fhandle('sampleoutput2.aavf', "w+")
writer = parser.Writer(out, aavf_obj)
records = list(aavf_obj)
for record in records:
writer.write_record(record)
writer.flush()
writer.close()
sample2 = TEST_PATH + "/sampleoutput2.aavf"
# initialize readers for iteration below
reader = parser.Reader(SAMPLE_FILE)
aavf_obj = reader.read_records()
reader2 = parser.Reader(sample2)
aavf_obj2 = reader2.read_records()
# iterate over sample file input and written output to see if they match
for left, right in zip(aavf_obj, aavf_obj2):
assert left.INFO == right.INFO, "left.INFO is %s and right.INFO is %s" \
% (left.INFO, right.INFO)
def test_walk(self):
"""
Walk through three readers simultaneously and make sure that the
output is identical.
"""
# easy case: all same sites
aavf1 = parser.Reader(SAMPLE_FILE).read_records()
aavf2 = parser.Reader(SAMPLE_FILE).read_records()
aavf3 = parser.Reader(SAMPLE_FILE).read_records()
number = 0
for trio in utils.walk_together(aavf1, aavf2, aavf3):
assert len(trio) == 3
assert trio[0] == trio[1]
assert trio[1] == trio[2]
number += 1
assert number == 7
def test_parse(self):
"""Test whether the INFO section can be parsed correctly."""
reader = parser.Reader(SAMPLE_FILE)
aavf_obj = reader.read_records()
record = next(aavf_obj)
assert record.INFO['RC'] == 'tca', "record.INFO['RC'] should be 'tca'" + \
", record.INFO is %s" % record.INFO
# the below two RESERVED_INFO constants in the INFO fields have a
# number of possible values that varies ior is unbounded. Thus, a list
# is returned.
assert record.INFO['AC'] == ['tAa']
assert record.INFO['ACF'] == [0.0031]
def test_write_to_file(self):
"""Test whether writes to file work as expected."""
reader = parser.Reader(SAMPLE_FILE)
aavf_obj = reader.read_records()
out = fhandle('sampleoutput3.aavf', "w+")
writer = parser.Writer(out, aavf_obj)
records = list(aavf_obj)
for record in records:
writer.write_record(record)
out.close()
reader1 = parser.Reader(TEST_PATH +
'/sampleoutput3.aavf').read_records()
reader2 = parser.Reader(SAMPLE_FILE).read_records()
assert len(list(reader1)) == len(list(reader2))
# all data lines should be read from the sample file
reader2 = parser.Reader(SAMPLE_FILE).read_records()
for left, right in zip(reader1, reader2):
assert left.INFO == right.INFO
def test_aavf_1_0(self):
"""Test with AAVF Version 1.0"""
reader = parser.Reader(SAMPLE_FILE)
aavf_obj = reader.read_records()
assert 'fileformat' in aavf_obj.metadata.keys(), "Metadata should contain fileformat," + \
"metadata dict is %s" % aavf_obj.metadata.items()
assert aavf_obj.metadata['fileformat'] == 'AAVFv1.0'
# test we can walk the file at least
for line in aavf_obj:
if line.POS == 103:
assert not line.is_filtered
else:
assert line.is_filtered
def summarize_sample_calls(in_file, aavf_files):
"""Provide a single tab delimited output of samples from AAVF inputs.
"""
out_file = os.path.join(os.getcwd(), "%s-calls.csv" % os.path.splitext(os.path.basename(in_file))[0])
with open(out_file, "w") as out_handle:
writer = csv.writer(out_handle)
writer.writerow(["sample", "gene", "pos", "ref", "alt", "altfreq", "altcount", "coverage",
"filter", "drug", "drugcat"])
for sample, aavf_file in aavf_files:
reader = parser.Reader(aavf_file)
for rec in reader.read_records():
writer.writerow([sample, rec.GENE, rec.POS, rec.REF, ";".join(rec.ALT),
rec.ALT_FREQ, rec.COVERAGE,
int(functools.reduce(operator.add, rec.INFO.get("ACC", []))),
";".join(rec.FILTER) if rec.FILTER else "pass",
";".join(rec.INFO.get("DRUG", [])), ";".join(rec.INFO.get("CAT", []))])
return out_file
def output_resistance_levels(aavf_file, xml_file, output_path):
"""
Parse aavf file to AAVF object.
Create XmlAsiTransformer.
Use transformer to evaluate drug resistance levels in the
AAVF object mutations.
Output drug resistance.
"""
records = list(parser.Reader(aavf_file).read_records())
mutations = defaultdict(list) # parse mutations from records
genes = XmlAsiTransformer(True).transform(open(xml_file, "r"))
output_file = output_path
# handles the case where the output_path was passed from somewhere
# other than to click, from the command line,
# e.g. from a test file
if isinstance(output_path, str):
output_file = open(output_path, "w+")
output_string = "#gene,drug class,drug,resistance level"
# create mutations list
for record in records:
if record.ALT[0] != "*":
mutations[record.GENE].append("%s%s" % (record.POS, record.ALT[0]))
for gene in mutations:
evaluated_gene = genes[gene].evaluate(mutations[gene],
StringMutationComparator(True))
for drug_class in evaluated_gene.get_evaluated_drug_classes():
for drug in drug_class.get_evaluated_drugs():
for condition in drug.get_evaluated_conditions():
definition = next(iter(condition.get_definitions()))
output_string += ("\n%s,%s,%s,%s" %
(gene, drug_class.get_drug_class().name,
drug.get_drug().name,
definition.get_text()))
output_file.write(output_string)
output_file.close()
return output_string
def test_read_from_stream(self):
"""Test whether reads from stream work as expected and if the AAVF
record object returned is correct."""
aavf = parser.Reader(open(SAMPLE_FILE, "r")).read_records()
record_list = [record for record in aavf]
assert isinstance(aavf, AAVF)
assert aavf.metadata.get("fileformat") == "AAVFv1.0", \
"fileformat should be AAVFv1.0, metadata is %s" % aavf.metadata
assert aavf.metadata.get("fileDate") == "20180501", \
"filedate should be 20180501, metadata is %s" % aavf.metadata
assert aavf.metadata.get("source") == "myProgramV1.0", \
"source should be myProgramV1.0, metadata is %s" % aavf.metadata
assert aavf.metadata.get("reference") == ["hxb2.fas"], \
"reference list should be [hxb2.fas], metadata is %s" % aavf.metadata
assert aavf.infos
assert aavf.filters
assert len(record_list) == 7
# all data lines should be the same as in the sample file
for record in record_list:
assert isinstance(record, Record)
def test_writer(self):
"""
Order of INFO fields should be compatible with the order of their
definition in the header and undefined fields should be last and in
alphabetical order.
"""
reader = parser.Reader(SAMPLE_FILE)
aavf_obj = reader.read_records()
out = StringIO()
writer = parser.Writer(out, aavf_obj)
for record in aavf_obj:
writer.write_record(record)
out.seek(0)
out_str = out.getvalue()
out.close()
definitions = []
for line in out_str.split('\n'):
if line.startswith('##INFO='):
definitions.append(line.split('ID=')[1].split(',')[0])
if not line or line.startswith('#'):
continue
fields = [f.split('=')[0] for f in line.split('\t')[7].split(';')]
self._assert_order(definitions, fields)
def annotate_aavf(in_file, hivdb_file, out_file):
"""Annotate an AAVF input file with drug resistance changes.
"""
res_genes = XmlAsiTransformer(True).transform(open(hivdb_file, "r"))
reader = parser.Reader(in_file)
aavf_obj = reader.read_records()
aavf_obj.infos["CAT"] = model.Info("CAT", ".", "String", "Drug resistance category", None, None)
aavf_obj.infos["DRUG"] = model.Info("DRUG", ".", "String", "Drug reistances", None, None)
with open(out_file, "w") as out_handle:
writer = parser.Writer(out_handle, aavf_obj)
for rec in aavf_obj:
if rec.POS not in rec.ALT:
rmuts = evaluate_resistance([rec], res_genes)
k = (rec.GENE, "%s%s%s" % (rec.REF, rec.POS, rec.ALT[0]))
if rmuts.get(k):
cats = []
drugs = []
for cat in rmuts.get(k).keys():
cats.append(cat)
drugs.extend(rmuts[k][cat])
rec.INFO["CAT"] = cats
rec.INFO["DRUG"] = drugs
writer.write_record(rec)
