Exemplos de filter_snvs_by_ld em Python

Exemplo n.º 1

Arquivo: test_ld.py Projeto: JoseBlanca/vcf_crumbs

    def test_check_backwards(self):
        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t703\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t2003\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t2403\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
'''
        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03, bonferroni=False)
        assert [s.pos for s in snvs] == [1, 702, 2002, 2402]

Exemplo n.º 2

Arquivo: test_ld.py Projeto: JoseBlanca/vcf_crumbs

    def test_cache(self):
        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t703\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t2003\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t3003\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t3403\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
'''
        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.001, bonferroni=False,
                                 snv_win=3)
        assert not list(snvs)

Exemplo n.º 3

Arquivo: test_ld.py Projeto: JoseBlanca/vcf_crumbs

    def test_filter(self):
        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
21\t3\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t'''
        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03)
        assert not list(snvs)

        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t3\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t'''
        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03)
        assert not list(snvs)

        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t703\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
'''
        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03, bonferroni=False)
        assert len(list(snvs)) == 2

        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t703\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
'''
        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03)
        assert not list(snvs)

        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t703\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t1/1\t1/1\t1/1\t1/1\t
20\t2003\t.\tG\tA\t29\tPASS\tNS=3\tGT\t1/1\t0/0\t1/1\t0/0\t1/1\t0/0\t1/1\t0/0\t
'''
        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03, bonferroni=False)
        assert [s.pos for s in snvs] == [1, 702]

        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0
20\t3\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0'''

        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03, bonferroni=False)
        assert not list(snvs)

        vcf = '''#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8
20\t2\t.\tG\tA\t29\tPASS\tNS=3\tGT\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0
20\t3\t.\tG\tA\t29\tPASS\tNS=3\tGT\t1/1\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0\t0/0'''

        vcf = StringIO(VCF_HEADER + vcf)
        snps = VCFReader(vcf).parse_snvs()
        snvs = filter_snvs_by_ld(snps, p_val=0.03, bonferroni=False)
        assert not list(snvs)