def test_gt_big_file(self):
''' Same test as above but with a larger vcf file
Tested:
SnpSift filter "( GEN[*].GT == '1/1' ) & ( GEN[*].DP > 100 )" testing3.vcf | grep -v '^#' | wc -l
'''
v = Vcf(here+'vcfs/testing3.vcf')
v.filter_vcf(['GT = 1/1', 'DP > 100'], how='any')
self.assertEqual(len(v.vcf), 257)
def test_pos_ranges(self):
''' Filter for variants between range
Tested:
SnpSift filter "( CHROM = '1') & ( POS > 2000 ) & ( POS < 2235601 )" testing2.vcf
'''
v = Vcf(here+'vcfs/testing2.vcf')
v.filter_vcf(['CHROM = 1', 'POS > 2000', 'POS < 2235601'])
answer = ['1:2234385-C/T', '1:2235243-C/T', '1:2235501-A/GGT']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_string(self):
''' Filter str fields
Tested:
SnpSift filter "( MEOW != 'ON' )" testing2.vcf
'''
v = Vcf(here+'vcfs/testing2.vcf')
v.filter_vcf(['MEOW != ON'])
answer = ['1:2234385-C/T', '1:2235901-A/G', '1:2235501-A/GGT']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_info_float_int(self):
''' Filter int and float fields
Tested:
SnpSift filter "( AF[0] < 0.1 ) & ( AC[0] > 2 )" testing2.vcf
'''
v = Vcf(here+'vcfs/testing2.vcf')
v.filter_vcf(['AF[0] < 0.1', 'AC[0] > 2'])
answer = ['1:2235901-A/G']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_info_depth(self):
''' Testing filtering the INFO DP field
Tested:
SnpSift filter "( DP > 100 )" testing.vcf
'''
v = Vcf(here+'vcfs/testing.vcf')
v.filter_vcf(['DEPTH > 100'])
answer = ['1:2234385-C/T', '1:2239999-A/G,T']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_AB(self):
''' Filter AB < 0.09
Tested:
I cannot find a tool to filter Vcfs by allele balance
'''
v = Vcf(here+'vcfs/testing2.vcf')
v.filter_vcf(['AB > 0', 'AB < 0.09'])
answer = ['1:2239999-A/G,T']
self.assertEqual(answer, v.vcf.index.tolist())
def test_gt_filter(self):
''' Simple genotype filter
Tested:
SnpSift filter "( GEN[*].GT == '1/1' ) & ( GEN[*].DP > 100 )" testing.vcf
'''
v = Vcf(here+'vcfs/testing.vcf')
v.filter_vcf(['GT = 1/1', 'DP > 100'], how='any')
answer = ['1:2235901-A/G', '1:2235501-A/GGT', '1:2239901-GA/G']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_loads(self):
''' Test numerous mandatory fields
Tested:
SnpSift filter "( FILTER != 'PASS' ) & ( ALT = 'G' ) & ( QUAL > 200 )" testing2.vcf
'''
v = Vcf(here+'vcfs/testing2.vcf')
v.filter_vcf(['FILTER != PASS', 'ALT = G', 'QUAL > 200'])
answer = ['1:2235792-A/G']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_or_operator(self):
''' Testing or operator
Tested:
SnpSift filter "( MEOW != 'ON' ) | ( LOLZ > 200 )" testing2.vcf
'''
v = Vcf(here+'vcfs/testing2.vcf')
v.filter_vcf(['MEOW != ON', 'LOLZ > 200'], op="|")
answer = ['1:2234385-C/T', '1:2235901-A/G', '1:2239999-A/G,T', '1:2235501-A/GGT']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_all_genotype(self):
''' Test filtering using the all flag in genotype fields
Tested:
SnpSift filter "( GEN[?].DP >= 50 ) & ( GEN[?].GQ >= 30 ) " testing.vcf
'''
v = Vcf(here+'vcfs/testing.vcf')
v.filter_vcf(['DP >= 50', 'GQ >= 30'], op='&', how='all')
answer = ['1:2235792-A/G']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_any_filtering(self):
''' Test filtering using the any flag
Tested:
SnpSift filter "( GEN[*].DP >= 50 ) & ( GEN[*].GQ >= 30 ) " testing.vcf
'''
v = Vcf(here+'vcfs/testing.vcf')
v.filter_vcf(['DP >= 50', 'GQ >= 30'], op='&', how='any')
answer = ['1:2235243-C/T', '1:2235792-A/G', '1:2235901-A/G',
'1:2239999-A/G,T', '1:2235501-A/GGT', '1:2239901-GA/G']
self.assertEqual(v.vcf.index.tolist(), answer)
def test_ultimate(self):
''' Test limits of filtering
Tested:
SnpSift filter "( GEN[*].GT == '0/1' ) & ( GEN[*].DP >= 50 ) & ( GEN[*].GQ >= 30 ) & ( AC[0] > 20 ) & ( CHROM = '1' ) & ( POS > 2235893 ) & ( ID =~ 'rs' )" testing3.vcf
'''
m = Vcf(here+'vcfs/testing3.vcf')
m.filter_vcf(['GT = 0/1', 'DP >= 50', 'GQ >= 30'])
m.filter_vcf(['AC[0] > 20'])
m.filter_vcf(['CHROM = 1', 'POS > 2235893', 'ID != .'])
answer = ['1:218519928-A/AAAAC', '1:218578726-ACTCT/A,ACTCTCT,ACT',
'1:218607557-G/T']
self.assertEqual(m.vcf.index.tolist(), answer)
#!/usr/bin/python3
from pdVCF.pdVCF import Vcf
import pandas as pd
import time
start = time.time()
tsv = pd.read_csv('vcfs/meow.vcf', sep="\t")
end = time.time() - start
print("{} seconds - read_cv()".format(round(end, 2)))
start = time.time()
vcf = Vcf('vcfs/testing3.vcf')
end = time.time() - start
print("{} seconds - vcf2dataframe()".format(round(end, 2)))