def main(args=None):
if args is None:
args = sys.argv[:]
print("Welcome to sequana_vcf_filter")
user_options = Options(prog="sequana_vcf_filter")
if "--version" in args:
import sequana
print(sequana.version)
sys.exit()
elif len(args) == 1 or "--help" in args:
user_options.parse_args(["prog", "--help"])
elif len(args) == 2:
class SimpleOpt():
pass
options = SimpleOpt()
options.input_filename = args[1]
else:
options = user_options.parse_args(args[1:])
# set the level
logger.level = options.level
vcf = VCF(options.input_filename)
vcf.vcf.filter_dict['QUAL'] = options.quality
vcf.vcf.apply_indel_filter = options.apply_indel_filter
vcf.vcf.apply_dp4_filter = options.apply_dp4_filter
vcf.vcf.apply_af1_filter = options.apply_af1_filter
vcf.vcf.dp4_minimum_depth = options.minimum_depth
vcf.vcf.dp4_minimum_depth_strand = options.minimum_depth_strand
vcf.vcf.dp4_minimum_ratio = options.minimum_ratio
vcf.vcf.minimum_af1 = options.minimum_af1
vcf.vcf.filter_dict['INFO'] = {}
vcf.vcf.filter_dict['QUAL'] = options.quality
for this in options.filter:
this = this[0]
signs = [">", "<", ">=", "<="]
for sign in signs:
if sign in this:
key, value = this.split(sign, 1)
key = key.strip()
value = sign.strip() + value.strip()
vcf.vcf.filter_dict['INFO'][key] = value
break
logger.info(vcf.vcf.filter_dict)
res = vcf.vcf.filter_vcf(options.output_filename,
output_filtered=options.output_filtered_filename)
print()
#print(res)
return res
def test_vcf_filter():
data = sequana_data("test_vcf_mpileup_4dot1.vcf")
v = VCF(data)
assert v.vcf.version == "4.1"
# Test the INFO set to {}
v.vcf.filter_dict['INFO'] = {}
v.vcf.filter_dict['QUAL'] = 50
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 308, 'unfiltered': 265}
# Test the & filter
v.vcf.filter_dict["QUAL"] = 0
v.vcf.filter_dict["INFO"] = {}
v.vcf.rewind()
v.vcf.filter_dict['INFO']['DP'] = ">40&<=80"
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 10, 'unfiltered': 563}
# check the | filter
v.vcf.filter_dict["QUAL"] = 0
v.vcf.filter_dict["INFO"] = {}
v.vcf.rewind()
v.vcf.filter_dict['INFO']['DP'] = "<40|>=80"
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 562, 'unfiltered': 11}
# check the array filter
v.vcf.filter_dict["QUAL"] = 0
v.vcf.filter_dict["INFO"] = {}
v.vcf.rewind()
v.vcf.filter_dict['INFO']['DP4[0]'] = "<2"
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 173, 'unfiltered': 400}
# Check the array access to one item
v.vcf.filter_dict["QUAL"] = 0
v.vcf.filter_dict["INFO"] = {}
v.vcf.rewind()
v.vcf.filter_dict['INFO']['DP4[2]'] = "<2"
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 199, 'unfiltered': 374}
# Check the sum of elements in an array
v.vcf.filter_dict["QUAL"] = 0
v.vcf.filter_dict["INFO"] = {}
v.vcf.rewind()
v.vcf.filter_dict['INFO']['sum(DP4[2], DP4[3])'] = "<4"
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 7, 'unfiltered': 566}
def test_indel():
data = sequana_data("test_vcf_mpileup_4dot1.vcf")
v = VCF(data)
variant = next(v.vcf)
assert v.vcf.is_indel(variant) is False
variant = next(v.vcf)
assert v.vcf.is_indel(variant) is False
variant = next(v.vcf)
assert v.vcf.is_indel(variant) is True
def test_af1():
data = sequana_data("test_vcf_mpileup_4dot1.vcf")
v = VCF(data)
variant = next(v.vcf)
variant.INFO['AF1'] = 1
assert v.vcf.is_valid_af1(variant) is True
variant.INFO['AF1'] = 0.5
assert v.vcf.is_valid_af1(variant) is False
# polymorphic case
variant = next(v.vcf)
variant.INFO['AF1'] = 1
assert v.vcf.is_valid_af1(variant) is False
#variant.INFO['AF1'] = 0.5
#assert v.vcf.is_valid_af1(variant) is True
v = VCF(data)
v.vcf.apply_af1_filter = True
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 391, 'unfiltered': 182}
def test_vcf_filter_freebayes():
data = sequana_data("test.vcf")
v = VCF(data)
v.hist_qual()
def test_vcf_filter_dp4():
data = sequana_data("test_vcf_mpileup_4dot1.vcf")
v = VCF(data)
variant = next(v.vcf)
def validate_variant_alternatate(variant):
# variant.ALT must be different from "." for this test
assert str(variant.ALT[0]).strip() != "."
# test minimum depth of alternate must be >= 4
variant.INFO['DP4'] = [0, 0, 2, 2]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75)
# here, not enough depth on alternate strand reverse or forward
variant.INFO['DP4'] = [0, 0, 4, 1]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
variant.INFO['DP4'] = [0, 0, 1, 4]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
# mimimum ratio must be > 0.75
variant.INFO['DP4'] = [25, 0, 75, 75]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is True
variant.INFO['DP4'] = [25, 25, 75,
74] # just below 0.75 for the alt reverse
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
variant.INFO['DP4'] = [25, 25, 74,
75] # just below 0.75 for the alt forward
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
# variant.ALT is equal to "A"
validate_variant_alternatate(variant)
def validate_variant_reference(variant):
# variant.ALT must be different from "." for this test
assert str(variant.ALT[0]).strip() == "."
# test minimum depth of alternate must be >= 4
variant.INFO['DP4'] = [2, 2, 0, 0]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75)
# here, not enough depth on alternate strand reverse or forward
variant.INFO['DP4'] = [4, 1, 0, 0]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
variant.INFO['DP4'] = [1, 4, 0, 0]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
# mimimum ratio must be > 0.75
variant.INFO['DP4'] = [75, 75, 25, 0]
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is True
variant.INFO['DP4'] = [75, 74, 25,
25] # just below 0.75 for the alt reverse
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
variant.INFO['DP4'] = [74, 75, 25,
25] # just below 0.75 for the alt forward
assert v.vcf.is_valid_dp4(variant, 4, 2, 0.75) is False
# variant.ALT is equal to "A"
variant.ALT[0].sequence = "."
validate_variant_reference(variant)
# Now, let us do the filtering with the vcf_filter method
v = VCF(data)
v.vcf.apply_dp4_filter = True
with TempFile() as fh:
res = v.vcf.filter_vcf(fh.name)
assert res == {'N': 573, 'filtered': 414, 'unfiltered': 159}
def main(args=None):
if args is None:
args = sys.argv[:]
print("Welcome to sequana_vcf_filter")
user_options = Options(prog="sequana_vcf_filter")
if len(args) == 1 or "--help" in args:
user_options.parse_args(["prog", "--help"])
elif len(args) == 2:
class SimpleOpt():
pass
options = SimpleOpt()
options.input_filename = args[1]
else:
options = user_options.parse_args(args[1:])
# set the level
logger.level = options.level
vcf = VCF(options.input_filename)
vcf.vcf.filter_dict['QUAL'] = options.quality
vcf.vcf.filter_dict['INFO'] = {}
print("------------------")
# Read filters from a file
if options.filter_file:
import configparser
cfg = configparser.RawConfigParser()
cfg.optionsxform = str
cfg.read(options.filter_file)
if cfg.has_section('filters'):
for key, value in cfg.items('filters'):
vcf.vcf.filter_dict["INFO"][key.upper()] = value
else:
raise ValueError("filter file must contain a section "
"[filters] use --help for more information")
if cfg.has_section('general'):
quality = cfg.getint('general', 'quality')
vcf.vcf.filter_dict['QUAL'] = quality
if options.quality != 0:
vcf.vcf.filter_dict['QUAL'] = options.quality
for this in options.filter:
this = this[0]
signs = [">", "<", ">=", "<="]
for sign in signs:
if sign in this:
key, value = this.split(sign)
key = key.strip()
value = sign.strip() + value.strip()
vcf.vcf.filter_dict['INFO'][key] = value
continue
print(vcf.vcf.filter_dict)
res = vcf.vcf.filter_vcf(options.output_filename,
output_filtered=options.output_filtered_filename)
print()
#print(res)
return res
def test_vcf_filter_freebayes():
data = sequana_data("test.vcf")
v = VCF(data)
v.hist_qual()