Python VcfPlugin.variants方法代碼示例

本文整理匯總了Python中puzzle.plugins.VcfPlugin.variants方法的典型用法代碼示例。如果您正苦於以下問題：Python VcfPlugin.variants方法的具體用法？Python VcfPlugin.variants怎麽用？Python VcfPlugin.variants使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類puzzle.plugins.VcfPlugin的用法示例。

在下文中一共展示了VcfPlugin.variants方法的10個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。

示例1: test_filters_no_filter

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
    def test_filters_no_filter(self, case_obj):
        plugin = VcfPlugin()
        plugin.add_case(case_obj)
        case_id = case_obj.case_id

        filters = {}
        result = plugin.variants(case_id, filters=filters, count=1000)
        
        assert result.nr_of_variants == 108

開發者ID:J35P312，項目名稱:puzzle，代碼行數:11，代碼來源:test_vcf_variant_mixin.py

示例2: test_variants_case_with_ped

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
def test_variants_case_with_ped():
    vcf_plugin = VcfPlugin(root_path=vcf, case_lines=individuals, case_type='ped')
    variants = vcf_plugin.variants(case_id='636808')
    variant = next(variants)
    assert variant['CHROM'] == 'X'
    assert int(variant['POS']) == 84563218
    assert variant['index'] == 1

    variant = next(variants)
    assert variant['CHROM'] == '2'
    assert int(variant['POS']) == 233349186
    assert variant['index'] == 2

開發者ID:brainstorm，項目名稱:puzzle，代碼行數:14，代碼來源:test_vcf.py

示例3: test_variants_case_no_ped

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
def test_variants_case_no_ped():
    vcf_plugin = VcfPlugin(root_path=vcf)
    variants = vcf_plugin.variants(case_id='hapmap.vcf')
    variant = next(variants)
    assert variant['CHROM'] == 'X'
    assert int(variant['POS']) == 84563218
    assert variant['index'] == 1

    variant = next(variants)
    assert variant['CHROM'] == '2'
    assert int(variant['POS']) == 233349186
    assert variant['index'] == 2

開發者ID:brainstorm，項目名稱:puzzle，代碼行數:14，代碼來源:test_vcf.py

示例4: test_filters_frequency

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
    def test_filters_frequency(self, case_obj):
        plugin = VcfPlugin()
        plugin.add_case(case_obj)
        case_id = case_obj.case_id

        filters = {'frequency':'0.001'}
        result = plugin.variants(case_id, filters=filters, count=1000)
        variants = result.variants
        nr_of_variants = result.nr_of_variants
        for variant_obj in variants:
            assert variant_obj.max_freq <= 0.001
        
        assert nr_of_variants == 88

開發者ID:J35P312，項目名稱:puzzle，代碼行數:15，代碼來源:test_vcf_variant_mixin.py

示例5: test_filters_impact_severities_high

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
    def test_filters_impact_severities_high(self, case_obj):
        plugin = VcfPlugin()
        plugin.add_case(case_obj)
        case_id = case_obj.case_id

        filters = {'impact_severities':['HIGH']}
        result = plugin.variants(case_id, filters=filters, count=1000)
        variants = result.variants
        nr_of_variants = result.nr_of_variants
        
        for variant_obj in variants:
            assert variant_obj.impact_severity == 'HIGH'
        
        assert nr_of_variants == 7

開發者ID:J35P312，項目名稱:puzzle，代碼行數:16，代碼來源:test_vcf_variant_mixin.py

示例6: test_filters_cadd

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
    def test_filters_cadd(self, case_obj):
        plugin = VcfPlugin()
        plugin.add_case(case_obj)
        case_id = case_obj.case_id

        filters = {'cadd':'20'}
        result = plugin.variants(case_id, filters=filters, count=1000)
        variants = result.variants
        nr_of_variants = result.nr_of_variants
        
        for variant_obj in variants:
            variant_obj.cadd_score >= 20
        
        assert nr_of_variants == 50

開發者ID:J35P312，項目名稱:puzzle，代碼行數:16，代碼來源:test_vcf_variant_mixin.py

示例7: test_filters_consequence

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
    def test_filters_consequence(self, case_obj):
        plugin = VcfPlugin()
        plugin.add_case(case_obj)
        case_id = case_obj.case_id

        filters = {'consequence':['frameshift_variant']}
        result = plugin.variants(case_id, filters=filters, count=1000)
        variants = result.variants
        nr_of_variants = result.nr_of_variants
        
        for variant_obj in variants:
            assert 'frameshift_variant' in variant_obj.consequences
        
        assert nr_of_variants == 4

開發者ID:J35P312，項目名稱:puzzle，代碼行數:16，代碼來源:test_vcf_variant_mixin.py

示例8: test_filters_gene_ids

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
    def test_filters_gene_ids(self, case_obj):
        plugin = VcfPlugin()
        plugin.add_case(case_obj)
        case_id = case_obj.case_id

        filters = {'gene_ids':['POF1B']}
        result = plugin.variants(case_id, filters=filters, count=1000)
        variants = result.variants
        nr_of_variants = result.nr_of_variants
        
        for variant_obj in variants:
            assert 'POF1B' in variant_obj.gene_symbols
        
        assert nr_of_variants == 1

開發者ID:J35P312，項目名稱:puzzle，代碼行數:16，代碼來源:test_vcf_variant_mixin.py

示例9: test_variants_case

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
def test_variants_case(case_obj):
    vcf_plugin = VcfPlugin()
    vcf_plugin.add_case(case_obj)
    #case_id is 'hapmap.vcf' since no ped file is given
    result = vcf_plugin.variants(case_id=case_obj.case_id)
    variants = result.variants
    variant = variants[0]
    assert variant['CHROM'] == 'X'
    assert int(variant['POS']) == 84563218
    assert variant['index'] == 1

    variant = variants[1]
    assert variant['CHROM'] == '2'
    assert int(variant['POS']) == 233349186
    assert variant['index'] == 2

開發者ID:J35P312，項目名稱:puzzle，代碼行數:17，代碼來源:test_vcf_variant_mixin.py

示例10: test_filters_range

# 需要導入模塊: from puzzle.plugins import VcfPlugin [as 別名]
# 或者: from puzzle.plugins.VcfPlugin import variants [as 別名]
    def test_filters_range(self, case_obj, indexed_vcf_file):
        plugin = VcfPlugin()
        case_obj.variant_source = indexed_vcf_file
        case_obj.compressed = True
        case_obj.tabix_index = True
        
        plugin.add_case(case_obj)
        case_id = case_obj.case_id
        start = 1771120
        end = 1771130

        filters = {'range':{'chromosome':'1', 'start':start, 'end':end}}
        result = plugin.variants(case_id, filters=filters, count=1000)
        variants = result.variants
        nr_of_variants = result.nr_of_variants
        
        for variant_obj in variants:
            assert variant_obj.start >= start
            assert variant_obj.stop <= end
        
        assert nr_of_variants == 1

開發者ID:J35P312，項目名稱:puzzle，代碼行數:23，代碼來源:test_vcf_variant_mixin.py

注：本文中的puzzle.plugins.VcfPlugin.variants方法示例由純淨天空整理自Github/MSDocs等開源代碼及文檔管理平台，相關代碼片段篩選自各路編程大神貢獻的開源項目，源碼版權歸原作者所有，傳播和使用請參考對應項目的License；未經允許，請勿轉載。