def test_rank_models():
"""Test to get the raw chromosome"""
variant_dict = get_variant_dict(info="GeneticModels=1:AD|AD_dn,2:AR_hom")
variant_line = get_variant_line(info="GeneticModels=1:AD|AD_dn,2:AR_hom")
plugin = Plugin(
name='genetic_models',
field='INFO',
data_type='string',
info_key="GeneticModels",
separators=[',', ':', '|'],
dict_entry=True,
string_rules={
'AD_dn':1,
'AD':2
}
)
dict_entry = plugin.get_value(
variant_dict=variant_dict,
dict_key='1'
)
line_entry = plugin.get_value(
variant_line=variant_line,
dict_key='1'
)
assert dict_entry == 'AD'
assert line_entry == 'AD'
def test_pos():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Pos', field='POS')
test_pos = '1000'
variant_line = get_variant_line(pos=test_pos)
variant_dict = get_variant_dict(pos=test_pos)
assert plugin.get_value(variant_line=variant_line) == test_pos
assert plugin.get_value(variant_dict=variant_dict) == test_pos
def test_chrom():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Chrom', field='CHROM')
test_chrom = '10'
variant_line = get_variant_line(chrom=test_chrom)
variant_dict = get_variant_dict(chrom=test_chrom)
assert plugin.get_value(variant_line=variant_line) == test_chrom
assert plugin.get_value(variant_dict=variant_dict) == test_chrom
def test_id_flag():
"""Test to get the raw chromosome"""
plugin = Plugin(name='ID', field='ID')
db_id = 'rs001'
variant_line = get_variant_line(db_id=db_id)
variant_dict = get_variant_dict(db_id=db_id)
assert plugin.get_value(variant_line=variant_line) == db_id
assert plugin.get_value(variant_dict=variant_dict) == db_id
def test_multiple_id_no_rule():
"""Test to get the raw chromosome"""
plugin = Plugin(name='ID', field='ID', data_type='flag')
db_id_1 = 'rs001'
db_id_2 = 'rs002'
db_id = "{0};{1}".format(db_id_1, db_id_2)
variant_line = get_variant_line(db_id=db_id)
variant_dict = get_variant_dict(db_id=db_id)
assert plugin.get_value(variant_line=variant_line) == True
assert plugin.get_value(variant_dict=variant_dict) == True
def test_flag():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='DB',
field='INFO',
info_key="DB",
data_type='flag',
)
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_value(variant_line=variant_line) == True
assert plugin.get_value(variant_dict=variant_dict) == True
def test_rank_score_with_key():
"""Test to get the raw chromosome"""
variant_dict = get_variant_dict(info="RankScore=1:12,2:11")
variant_line = get_variant_line(info="RankScore=1:12,2:11")
plugin = Plugin(
name='rank_score',
data_type='integer',
field='INFO',
info_key="RankScore",
separators=[',', ':'],
dict_entry=True
)
dict_entry = plugin.get_value(
variant_dict=variant_dict,
dict_key='1'
)
line_entry = plugin.get_value(
variant_line=variant_line,
dict_key='1'
)
assert dict_entry == 12
assert line_entry == 12
def test_1000G_float():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='thousand_g',
field='INFO',
info_key="1000GAF",
separators=[','],
data_type='float',
)
test_value = 0.744609
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_value(variant_line=variant_line) == test_value
assert plugin.get_value(variant_dict=variant_dict) == test_value
def test_1000G_record_rule():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='thousand_g',
field='INFO',
info_key="1000GAF",
separators=[','],
data_type='float',
record_rule='min',
)
info = "1000GAF=0.744609,0.02;AC=2;AF=1.00;AN=2"
variant_line = get_variant_line(info=info)
variant_dict = get_variant_dict(info=info)
assert plugin.get_value(variant_line=variant_line) == 0.02
assert plugin.get_value(variant_dict=variant_dict) == 0.02
def test_filter_min_rule():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='Filter',
field='FILTER',
data_type='string',
string_rules={
'PASS':2,
'NOT_PASS':1
},
record_rule='min'
)
filt = "PASS;NOT_PASS"
variant_line = get_variant_line(filt=filt)
variant_dict = get_variant_dict(filt=filt)
assert plugin.get_value(variant_line=variant_line) == 'NOT_PASS'
assert plugin.get_value(variant_dict=variant_dict) == 'NOT_PASS'
def filter(variant_file, annotation, threshold, discard, greater, silent,
outfile):
"""
Filter vcf variants.
Filter variants based on their annotation
"""
logger.info("Running genmod filter version {0}".format(__version__))
variant_file = get_file_handle(variant_file)
start_time_analysis = datetime.now()
logger.info("Initializing a Header Parser")
head = HeaderParser()
for line in variant_file:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
#Add the first variant to the iterator
variant_file = itertools.chain([line], variant_file)
header_line = head.header
if not annotation in head.info_dict:
logger.warning(
"Annotation {0} not specified in header".format(annotation))
logger.info("Please check VCF file")
logger.info("Exiting...")
sys.exit(1)
logger.info(
"Building a plugin from extract_vcf for {0}".format(annotation))
annotation_plugin = Plugin(name=annotation,
field='INFO',
info_key=annotation,
separators=[','],
record_rule='min',
data_type='float')
logger.debug("Plugin=(field={0},info_key={1},separators={2},record_rule={3}"\
",data_type={4})".format('INFO', annotation, "','", 'min', 'float'))
print_headers(head=head, outfile=outfile, silent=silent)
nr_of_variants = 0
nr_of_passed_variants = 0
for variant in variant_file:
nr_of_variants += 1
keep_variant = False
value = annotation_plugin.get_value(variant_line=variant)
logger.debug("Found value {0}".format(value))
if value:
if greater:
if value > threshold:
keep_variant = True
else:
if value < threshold:
keep_variant = True
else:
if not discard:
keep_variant = True
if keep_variant:
logger.debug("Keeping variant")
nr_of_passed_variants += 1
print_variant(variant_line=variant,
outfile=outfile,
mode='vcf',
silent=silent)
else:
logger.debug("Discarding variant")
logger.info("Number of variants in file {0}".format(nr_of_variants))
logger.info(
"Number of variants passing filter {0}".format(nr_of_passed_variants))
logger.info(
"Number of variants filtered {0}".format(nr_of_variants -
nr_of_passed_variants))
def filter(variant_file, annotation, threshold, discard, greater, silent, outfile):
"""
Filter vcf variants.
Filter variants based on their annotation
"""
logger.info("Running genmod filter version {0}".format(__version__))
start_time_analysis = datetime.now()
logger.info("Initializing a Header Parser")
head = HeaderParser()
for line in variant_file:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
#Add the first variant to the iterator
variant_file = itertools.chain([line], variant_file)
header_line = head.header
if not annotation in head.info_dict:
logger.warning("Annotation {0} not specified in header".format(annotation))
logger.info("Please check VCF file")
logger.info("Exiting...")
sys.exit(1)
logger.info("Building a plugin from extract_vcf for {0}".format(annotation))
annotation_plugin = Plugin(
name=annotation,
field='INFO',
info_key=annotation,
separators = [','],
record_rule = 'min',
data_type = 'float'
)
logger.debug("Plugin=(field={0},info_key={1},separators={2},record_rule={3}"\
",data_type={4})".format('INFO', annotation, "','", 'min', 'float'))
print_headers(head=head, outfile=outfile, silent=silent)
nr_of_variants = 0
nr_of_passed_variants = 0
for variant in variant_file:
nr_of_variants += 1
keep_variant = False
value = annotation_plugin.get_value(variant_line=variant)
logger.debug("Found value {0}".format(value))
if value:
if greater:
if value > threshold:
keep_variant = True
else:
if value < threshold:
keep_variant = True
else:
if not discard:
keep_variant = True
if keep_variant:
logger.debug("Keeping variant")
nr_of_passed_variants += 1
print_variant(
variant_line=variant,
outfile=outfile,
mode='vcf',
silent=silent
)
else:
logger.debug("Discarding variant")
logger.info("Number of variants in file {0}".format(nr_of_variants))
logger.info("Number of variants passing filter {0}".format(nr_of_passed_variants))
logger.info("Number of variants filtered {0}".format(
nr_of_variants - nr_of_passed_variants))
