def test_var_subtype(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
subtype = var.var_subtype
if var.POS == 14370:
self.assertEqual("ts", subtype)
if var.POS == 17330:
self.assertEqual("tv", subtype)
if var.POS == 1110696:
self.assertEqual("unknown", subtype)
if var.POS == 1230237:
self.assertEqual("del", subtype)
elif var.POS == 1234567:
self.assertEqual("unknown", subtype)
reader.close()
# SV tests
reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
for var in reader:
subtype = var.var_subtype
if var.POS == 2827693:
self.assertEqual("DEL", subtype)
if var.POS == 321682:
self.assertEqual("DEL", subtype)
if var.POS == 14477084:
self.assertEqual("DEL:ME:ALU", subtype)
if var.POS == 9425916:
self.assertEqual("INS:ME:L1", subtype)
elif var.POS == 12665100:
self.assertEqual("DUP", subtype)
elif var.POS == 18665128:
self.assertEqual("DUP:TANDEM", subtype)
reader.close()
def test_walk(self):
# easy case: all same sites
reader1 = cyvcf.Reader(fh('example-4.0.vcf'))
reader2 = cyvcf.Reader(fh('example-4.0.vcf'))
reader3 = cyvcf.Reader(fh('example-4.0.vcf'))
n = 0
for x in utils.walk_together(reader1, reader2, reader3):
assert len(x) == 3
assert (x[0] == x[1]) and (x[1] == x[2])
n += 1
assert n == 5
# artificial case 2 from the left, 2 from the right, 2 together, 1 from the right, 1 from the left
expected = 'llrrttrl'
reader1 = cyvcf.Reader(fh('walk_left.vcf'))
reader2 = cyvcf.Reader(fh('example-4.0.vcf'))
for ex, recs in zip(expected, utils.walk_together(reader1, reader2)):
if ex == 'l':
assert recs[0] is not None
assert recs[1] is None
if ex == 'r':
assert recs[1] is not None
assert recs[0] is None
if ex == 't':
assert recs[0] is not None
assert recs[1] is not None
def test_sv_end(self):
reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
for var in reader:
sv_end = var.sv_end
if var.POS == 2827693:
self.assertEqual(2827680, sv_end)
if var.POS == 321682:
self.assertEqual(321887, sv_end)
if var.POS == 14477084:
self.assertEqual(14477381, sv_end)
if var.POS == 9425916:
self.assertEqual(9425916, sv_end)
elif var.POS == 12665100:
self.assertEqual(12686200, sv_end)
elif var.POS == 18665128:
self.assertEqual(18665204, sv_end)
reader.close()
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
sv_end = var.sv_end
if var.POS == 14370:
self.assertEqual(None, sv_end)
if var.POS == 17330:
self.assertEqual(None, sv_end)
if var.POS == 1110696:
self.assertEqual(None, sv_end)
if var.POS == 1230237:
self.assertEqual(None, sv_end)
elif var.POS == 1234567:
self.assertEqual(None, sv_end)
reader.close()
def test_var_type(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
type = var.var_type
if var.POS == 14370:
self.assertEqual("snp", type)
if var.POS == 17330:
self.assertEqual("snp", type)
if var.POS == 1110696:
self.assertEqual("snp", type)
if var.POS == 1230237:
self.assertEqual("indel", type)
elif var.POS == 1234567:
self.assertEqual("indel", type)
reader.close()
# SV tests
reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
for var in reader:
type = var.var_type
if var.POS == 2827693:
self.assertEqual("sv", type)
if var.POS == 321682:
self.assertEqual("sv", type)
if var.POS == 14477084:
self.assertEqual("sv", type)
if var.POS == 9425916:
self.assertEqual("sv", type)
elif var.POS == 12665100:
self.assertEqual("sv", type)
elif var.POS == 18665128:
self.assertEqual("sv", type)
reader.close()
def test_is_sv_precise(self):
reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
for var in reader:
is_precise = var.is_sv_precise
if var.POS == 2827693:
self.assertEqual(True, is_precise)
if var.POS == 321682:
self.assertEqual(False, is_precise)
if var.POS == 14477084:
self.assertEqual(False, is_precise)
if var.POS == 9425916:
self.assertEqual(False, is_precise)
elif var.POS == 12665100:
self.assertEqual(False, is_precise)
elif var.POS == 18665128:
self.assertEqual(False, is_precise)
reader.close()
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
is_precise = var.is_sv_precise
if var.POS == 14370:
self.assertEqual(False, is_precise)
if var.POS == 17330:
self.assertEqual(False, is_precise)
if var.POS == 1110696:
self.assertEqual(False, is_precise)
if var.POS == 1230237:
self.assertEqual(False, is_precise)
elif var.POS == 1234567:
self.assertEqual(False, is_precise)
reader.close()
def test_null_mono(self):
# null qualities were written as blank, causing subsequent parse to fail
print os.path.abspath(
os.path.join(os.path.dirname(__file__), 'null_genotype_mono.vcf'))
p = cyvcf.Reader(fh('null_genotype_mono.vcf'))
assert p.samples
out = StringIO()
writer = cyvcf.Writer(out, p)
map(writer.write_record, p)
out.seek(0)
print out.getvalue()
p2 = cyvcf.Reader(out)
rec = p2.next()
assert rec.samples
def test_num_calls(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
num_calls = (var.num_hom_ref + var.num_hom_alt + \
var.num_het + var.num_unknown)
self.assertEqual(len(var.samples), num_calls)
reader.close()
def testApplyFilter(self):
s, out = subprocess.getstatusoutput(
'python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq'
)
#print out
assert s == 0
buf = StringIO()
buf.write(out)
buf.seek(0)
print(buf.getvalue())
reader = cyvcf.Reader(buf)
# check filter got into output file
assert 'sq30' in reader.filters
print(reader.filters)
# check sites were filtered
n = 0
for r in reader:
if r.QUAL < 30:
assert 'sq30' in r.FILTER
n += 1
else:
assert r.FILTER is None or 'sq30' not in r.FILTER
assert n == 2
def testWrite(self):
reader = cyvcf.Reader(fh('gatk.vcf'))
out = StringIO()
writer = cyvcf.Writer(out, reader)
records = list(reader)
map(writer.write_record, records)
out.seek(0)
reader2 = cyvcf.Reader(out)
self.assertEquals(reader.samples, reader2.samples)
self.assertEquals(reader.formats, reader2.formats)
self.assertEquals(reader.infos, reader2.infos)
for l, r in zip(records, reader2):
self.assertEquals(l.samples, r.samples)
def testParse(self):
reader = cyvcf.Reader(fh('freebayes.vcf'))
print(reader.samples)
self.assertEqual(len(reader.samples), 7)
n = 0
for r in reader:
n += 1
for x in r:
assert x
assert n == self.n_calls
def test_gt_alt_depths(self):
reader = cyvcf.Reader(fh('gatk.vcf'))
for var in reader:
gt_alt_depths = [s.gt_alt_depth for s in var.samples]
if var.POS == 42522392:
self.assertEqual([0, 107, 77, 0, 1, 0, 0], gt_alt_depths)
elif var.POS == 42522613:
self.assertEqual([4, 127, 0, 85, 132, 135, 126], gt_alt_depths)
elif var.POS == 42527891:
self.assertEqual([-1, 7, 3, 11, 16, 14, 11], gt_alt_depths)
def test_gt_quals(self):
reader = cyvcf.Reader(fh('gatk.vcf'))
for var in reader:
gt_quals = [s.gt_qual for s in var.samples]
if var.POS == 42522392:
self.assertEqual([18.04, 99, 99, 99, 99, 99, 99], gt_quals)
elif var.POS == 42522613:
self.assertEqual([62.64, 99, 99, 99, 99, 99, 99], gt_quals)
elif var.POS == 42527891:
self.assertEqual([-1, 13.70, 5.97, 31.42, 49.09, 52.10, 12.71],
gt_quals)
def test_gt_bases(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
gt_bases = [s.gt_bases for s in var.samples]
if var.POS == 14370:
self.assertEqual(['G|G', 'A|G', 'A/A'], gt_bases)
elif var.POS == 17330:
self.assertEqual(['T|T', 'T|A', 'T/T'], gt_bases)
elif var.POS == 1110696:
self.assertEqual(['G|T', 'T|G', 'T/T'], gt_bases)
elif var.POS == 1230237:
self.assertEqual(['T|T', 'T|T', 'T/T'], gt_bases)
elif var.POS == 1234567:
self.assertEqual([None, 'GTCT/GTACT', 'G/G'], gt_bases)
def test_call_rate(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
call_rate = var.call_rate
if var.POS == 14370:
self.assertEqual(3.0 / 3.0, call_rate)
if var.POS == 17330:
self.assertEqual(3.0 / 3.0, call_rate)
if var.POS == 1110696:
self.assertEqual(3.0 / 3.0, call_rate)
if var.POS == 1230237:
self.assertEqual(3.0 / 3.0, call_rate)
elif var.POS == 1234567:
self.assertEqual(2.0 / 3.0, call_rate)
def test_aaf(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
aaf = var.aaf
if var.POS == 14370:
self.assertEqual(3.0 / 6.0, aaf)
if var.POS == 17330:
self.assertEqual(1.0 / 6.0, aaf)
if var.POS == 1110696:
self.assertEqual(None, aaf)
if var.POS == 1230237:
self.assertEqual(0.0 / 6.0, aaf)
elif var.POS == 1234567:
self.assertEqual(None, aaf)
def test_pi(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
pi = var.nucl_diversity
if var.POS == 14370:
self.assertEqual(6.0 / 10.0, pi)
if var.POS == 17330:
self.assertEqual(1.0 / 3.0, pi)
if var.POS == 1110696:
self.assertEqual(None, pi)
if var.POS == 1230237:
self.assertEqual(0.0 / 6.0, pi)
elif var.POS == 1234567:
self.assertEqual(None, pi)
def test_is_deletion(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
is_del = var.is_deletion
if var.POS == 14370:
self.assertEqual(False, is_del)
if var.POS == 17330:
self.assertEqual(False, is_del)
if var.POS == 1110696:
self.assertEqual(False, is_del)
if var.POS == 1230237:
self.assertEqual(True, is_del)
elif var.POS == 1234567:
self.assertEqual(False, is_del)
def test_gt_ref_depths(self):
reader = cyvcf.Reader(fh('gatk.vcf'))
for var in reader:
gt_ref_depths = [s.gt_ref_depth for s in var.samples]
if var.POS == 42522392:
self.assertEqual([6, 138, 169, 249, 248, 250, 250],
gt_ref_depths)
elif var.POS == 42522613:
self.assertEqual([13, 118, 241, 161, 110, 106, 116],
gt_ref_depths)
elif var.POS == 42527891:
self.assertEqual([-1, 238, 246, 239, 232, 233, 238],
gt_ref_depths)
def use_cyvcf(vcf_file):
""" Not installing (py3 not supported, py2 installs but import doesn't work)
"""
import cyvcf # need to reinstall instead of pyvcf
import gzip
f = gzip.open(vcf_file) if vcf_file.endswith('.gz') else open(vcf_file)
with f as f:
vcf_reader = cyvcf.Reader(f)
vcf_writer = cyvcf.Writer(sys.stdout, vcf_reader)
for rec in vcf_reader:
msi_fail = proc_fields(rec.REF, rec.ALT[0], rec.samples[0]['AF'],
rec.INFO['MSI'])
if msi_fail:
rec.FILTER.append('MSI_FAIL')
vcf_writer.write_record(rec)
def test_is_snp(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
is_snp = var.is_snp
if var.POS == 14370:
self.assertEqual(True, is_snp)
if var.POS == 17330:
self.assertEqual(True, is_snp)
if var.POS == 1110696:
self.assertEqual(True, is_snp)
if var.POS == 1230237:
self.assertEqual(False, is_snp)
elif var.POS == 1234567:
self.assertEqual(False, is_snp)
reader.close()
def test_phased(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
phases = var.gt_phases
print(var)
if var.POS == 14370:
self.assertEqual([True, True, False], phases)
if var.POS == 17330:
self.assertEqual([True, True, False], phases)
if var.POS == 1110696:
self.assertEqual([True, True, False], phases)
if var.POS == 1230237:
self.assertEqual([True, True, False], phases)
elif var.POS == 1234567:
self.assertEqual([False, False, False], phases)
def testApplyMultipleFilters(self):
s, out = subprocess.getstatusoutput(
'python scripts/vcf_filter.py --site-quality 30 '
'--genotype-quality 50 test/example-4.0.vcf sq mgq')
assert s == 0
#print out
buf = StringIO()
buf.write(out)
buf.seek(0)
reader = cyvcf.Reader(buf)
print(reader.filters)
assert 'mgq50' in reader.filters
assert 'sq30' in reader.filters
def test_vcf_4_1_sv(self):
return
reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
assert 'SVLEN' in reader.infos
# test we can walk the file at least
for r in reader:
print(r)
for c in r:
print(c)
assert c
# asserting False while I work out what to check
assert False
def test_vcf_4_1(self):
return
reader = cyvcf.Reader(fh('example-4.1.vcf'))
self.assertEqual(reader.metadata['fileformat'], 'VCFv4.1')
# contigs were added in vcf4.1
# probably need to add a reader.contigs attribute
assert 'contig' in reader.metadata
# test we can walk the file at least
for r in reader:
for c in r:
assert c
# asserting False while I work out what to check
assert False
def test_gt_types(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
for s in var:
print(s.data)
gt_types = [s.gt_type for s in var.samples]
if var.POS == 14370:
self.assertEqual([0, 1, 3], gt_types)
elif var.POS == 17330:
self.assertEqual([0, 1, 0], gt_types)
elif var.POS == 1110696:
self.assertEqual([1, 1, 3], gt_types)
elif var.POS == 1230237:
self.assertEqual([0, 0, 0], gt_types)
elif var.POS == 1234567:
self.assertEqual([None, 1, 3], gt_types)
def test_gt_depths(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
for var in reader:
for s in var:
print(s.data)
gt_depths = [s.gt_depth for s in var.samples]
if var.POS == 14370:
self.assertEqual([1, 8, 5], gt_depths)
elif var.POS == 17330:
self.assertEqual([3, 5, 3], gt_depths)
elif var.POS == 1110696:
self.assertEqual([6, 0, 4], gt_depths)
elif var.POS == 1230237:
self.assertEqual([7, 4, 2], gt_depths)
elif var.POS == 1234567:
self.assertEqual([4, 2, 3], gt_depths)
def check_existing_vcf_info_tags(input_vcf, pcgr_directory, logger):
"""
Function that compares the INFO tags in the query VCF and the INFO tags generated by PCGR
If any coinciding tags, an error will be returned
"""
vep_infotags_desc = pcgrutils.read_infotag_file(
os.path.join(pcgr_directory, 'data', 'vep_infotags.tsv'))
pcgr_infotags_desc = pcgrutils.read_infotag_file(
os.path.join(pcgr_directory, 'data', 'pcgr_infotags.tsv'))
vcfanno_tags = {}
for db in [
'intogen_driver_mut', 'dbsnp', 'oneKG', 'docm', 'exac', 'gnomad',
'civic', 'cbmdb', 'dbnsfp', 'clinvar', 'icgc', 'cosmic'
]:
vcfanno_tag_file = os.path.join(pcgr_directory, 'data', str(db),
str(db) + '.vcfanno.vcf_info_tags.txt')
try:
f = open(vcfanno_tag_file, 'r')
for line in f:
if line.startswith('##INFO'):
tag = re.sub(r'##INFO=<ID=', '',
str(line.rstrip().split(',')[0]))
vcfanno_tags[tag] = 1
except IOError:
logger.error('File ' + str(vcfanno_tag_file) + ' does not exist')
vcf_reader = cyvcf.Reader(open(input_vcf, 'r'))
logger.info(
'Checking if existing INFO tags of query VCF file coincide with PCGR INFO tags'
)
ret = 1
for k in vcf_reader.infos.keys():
if k in vep_infotags_desc.keys() or k in pcgr_infotags_desc.keys(
) or k in vcfanno_tags.keys() or k == 'EFFECT_PREDICTIONS':
logger.error(
'INFO tag ' + str(k) +
' in the query VCF coincides with a VCF annotation tag produced by PCGR - please remove or rename this tag in your query VCF'
)
ret = -1
return ret
def test_vcf_4_0(self):
reader = cyvcf.Reader(fh('example-4.0.vcf'))
assert reader.metadata['fileformat'] == 'VCFv4.0'
# test we can walk the file at least
for r in reader:
if r.POS == 1230237:
assert r.is_monomorphic
else:
assert not r.is_monomorphic
if 'AF' in r.INFO:
self.assertEqual(type(r.INFO['AF']), type([]))
for c in r:
assert c
# issue 19, in the example ref the GQ is length 1
if c.called:
self.assertEqual(type(c.data['GQ']), type(1))
if 'HQ' in c.data and c.data['HQ'] is not None:
self.assertEqual(type(c.data['HQ']), type([]))
#!/usr/bin/python import sys import cyvcf if __name__ == "__main__": if len(sys.argv) != 2: print "Usage: python %s <in.vcf>" % sys.argv[0] sys.exit() invcf = sys.argv[1] vcf_reader = cyvcf.Reader(open(invcf, 'rb')) for record in vcf_reader: print record
def vcf2tsv(query_vcf, out_tsv):
vcf_reader = cyvcf.Reader(open(query_vcf, 'r'))
f_out = open(out_tsv, 'w')
header_line = get_tsv_header(vcf_reader)
f_out.write(header_line + '\n')
for rec in vcf_reader:
alt = ",".join(str(n) for n in rec.ALT)
qual = '.'
rec_id = str(rec.ID)
if rec.ID is None:
rec_id = '.'
if not rec.QUAL is None:
qual = str(rec.QUAL)
rec_filter = str(rec.FILTER)
if type(rec.FILTER) is list:
if len(rec.FILTER) == 0:
rec_filter = 'PASS'
elif len(rec.FILTER) == 1:
rec_filter = str(rec.FILTER[0])
else:
rec_filter = str(';'.join(str(n) for n in rec.FILTER))
else:
if rec.FILTER is None:
rec_filter = 'PASS'
fixed_fields_string = str(rec.CHROM) + '\t' + str(
rec.POS) + '\t' + str(rec_id) + '\t' + str(rec.REF) + '\t' + str(
alt) + '\t' + str(qual) + '\t' + str(rec_filter)
infocolumn = []
for keyw in sorted(vcf_reader.infos.keys()):
if rec.INFO.has_key(keyw):
#print str(keyw) + '\t' + str(rec.INFO[keyw])
if vcf_reader.infos[keyw][2] == 'Flag':
if rec.INFO[keyw] == 1 or rec.INFO[keyw] == True:
infocolumn.append('True')
else:
infocolumn.append('False')
elif vcf_reader.infos[str(
keyw)][2] == 'Float' or vcf_reader.infos[str(
keyw)][2] == 'Integer':
if type(rec.INFO[str(keyw)]) is list:
infocolumn.append(",".join(
str(n) for n in rec.INFO[str(keyw)]))
else:
if re.search(r'^\[(.|\s)+\]$', str(rec.INFO[keyw])):
tmp = re.sub(r'\[|\]|\'|\s{1,}', '',
rec.INFO[keyw])
infocolumn.append(str(tmp))
else:
infocolumn.append(str(rec.INFO[str(keyw)]))
else:
if type(rec.INFO[keyw]) is list:
all_vals = []
for m in rec.INFO[str(keyw)]:
if m is None:
all_vals.append('NA')
else:
all_vals.append(m)
infocolumn.append(str(','.join(all_vals)))
else:
## For some reason(?) some lists are parsed into string objects by PyVCF
if re.search(r'^\[(.|\s)+\]$', str(rec.INFO[keyw])):
#print str(rec.INFO[keyw])
tmp = re.sub(r'\[|\]|\'|\s{1,}', '',
rec.INFO[keyw])
#print str(tmp)
infocolumn.append(str(tmp))
else:
infocolumn.append(str(rec.INFO[str(keyw)]))
else:
infocolumn.append('NA')
infostring = '\t'.join(infocolumn)
i = 0
if len(vcf_reader.samples) > 0:
while i < len(vcf_reader.samples):
genotype_values = []
skip_null_sample = False
depth_tumor_non_zero = False
depth_control_non_zero = False
for elem in sorted(rec.FORMAT.split(':')):
p = rec.samples[int(i)][str(elem)]
if isinstance(p, list):
genotype_values.append(','.join(map(str, p)))
else:
if not p:
if str(elem) == 'GT':
skip_null_sample = True
genotype_values.append('./.')
else:
if p is None:
p = '.'
genotype_values.append(str(p))
else:
if elem == 'GT' and p == './.':
skip_null_sample = True
genotype_values.append(str(p))
sample_genotype_data = '\t'.join(genotype_values)
if skip_null_sample is False:
tsvline = fixed_fields_string + '\t' + infostring + '\t' + str(
vcf_reader.samples[i]
) + '\t' + sample_genotype_data + '\n'
f_out.write(tsvline)
i = i + 1
else:
tsvline = fixed_fields_string + '\t' + infostring + '\n'
f_out.write(tsvline)
f_out.close()
