def test_gt_call_no_header(): """Test to get the raw chromosome""" plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT') variant_line = get_variant_line() with pytest.raises(IOError): plugin.get_raw_entry(variant_line=variant_line, individual_id='ADM1003A3')
def test_gt_call_no_individual(): """Test to get the raw chromosome""" plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT') vcf_header = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'ADM1003A3'] variant_line = get_variant_line() variant_dict = get_variant_dict() with pytest.raises(IOError): plugin.get_raw_entry(variant_line=variant_line, vcf_header=vcf_header) with pytest.raises(IOError): plugin.get_raw_entry(variant_dict=variant_dict, vcf_header=vcf_header)
def test_id(): """Test to get the raw chromosome""" plugin = Plugin(name='ID', field='ID') db_id = 'rs001' variant_line = get_variant_line(db_id=db_id) variant_dict = get_variant_dict(db_id=db_id) assert plugin.get_raw_entry(variant_line=variant_line) == db_id assert plugin.get_raw_entry(variant_dict=variant_dict) == db_id
def test_pos(): """Test to get the raw chromosome""" plugin = Plugin(name='Pos', field='POS') test_pos = '1000' variant_line = get_variant_line(pos=test_pos) variant_dict = get_variant_dict(pos=test_pos) assert plugin.get_raw_entry(variant_line=variant_line) == test_pos assert plugin.get_raw_entry(variant_dict=variant_dict) == test_pos
def test_chrom(): """Test to get the raw chromosome""" plugin = Plugin(name='Chrom', field='CHROM') test_chrom = '10' variant_line = get_variant_line(chrom=test_chrom) variant_dict = get_variant_dict(chrom=test_chrom) assert plugin.get_raw_entry(variant_line=variant_line) == test_chrom assert plugin.get_raw_entry(variant_dict=variant_dict) == test_chrom
def test_gt_call(): """Test to get the raw chromosome""" plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT') vcf_header = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'ADM1003A3'] variant_line = get_variant_line() variant_dict = get_variant_dict() assert plugin.get_raw_entry( variant_line=variant_line, vcf_header=vcf_header, individual_id='ADM1003A3') == '1/1' assert plugin.get_raw_entry( variant_dict=variant_dict, vcf_header=vcf_header, individual_id='ADM1003A3') == '1/1'
def test_CLNSIG(): """Test to get the raw chromosome""" plugin = Plugin(name='Clnsig', field='INFO', info_key="CLNSIG") test_value = '255,10' variant_line = get_variant_line() variant_dict = get_variant_dict() assert plugin.get_raw_entry(variant_line=variant_line) == test_value assert plugin.get_raw_entry(variant_dict=variant_dict) == test_value
def test_format(): """Test to get the raw chromosome""" plugin = Plugin(name='Format', field='FORMAT') form = 'GT:AD:GQ:PL' variant_line = get_variant_line(form=form) variant_dict = get_variant_dict(form=form) assert plugin.get_raw_entry(variant_line=variant_line) == form assert plugin.get_raw_entry(variant_dict=variant_dict) == form
def test_filter(): """Test to get the raw chromosome""" plugin = Plugin(name='Filter', field='FILTER') filt = 'PASS' variant_line = get_variant_line(filt=filt) variant_dict = get_variant_dict(filt=filt) assert plugin.get_raw_entry(variant_line=variant_line) == filt assert plugin.get_raw_entry(variant_dict=variant_dict) == filt
def test_qual(): """Test to get the raw chromosome""" plugin = Plugin(name='QUAL', field='QUAL') qual = '1234.5' variant_line = get_variant_line(qual=qual) variant_dict = get_variant_dict(qual=qual) assert plugin.get_raw_entry(variant_line=variant_line) == qual assert plugin.get_raw_entry(variant_dict=variant_dict) == qual
def test_alt(): """Test to get the raw chromosome""" plugin = Plugin(name='alt', field='ALT') alt = 'A' variant_line = get_variant_line(alt=alt) variant_dict = get_variant_dict(alt=alt) assert plugin.get_raw_entry(variant_line=variant_line) == alt assert plugin.get_raw_entry(variant_dict=variant_dict) == alt
def test_ref(): """Test to get the raw chromosome""" plugin = Plugin(name='ref', field='REF') ref = 'rs001' variant_line = get_variant_line(ref=ref) variant_dict = get_variant_dict(ref=ref) assert plugin.get_raw_entry(variant_line=variant_line) == ref assert plugin.get_raw_entry(variant_dict=variant_dict) == ref
def test_1000G(): """Test to get the raw chromosome""" plugin = Plugin(name='thousand_g', field='INFO', info_key="1000GAF") variant_line = get_variant_line() variant_dict = get_variant_dict() test_value = '0.744609' assert plugin.get_raw_entry(variant_line=variant_line) == test_value assert plugin.get_raw_entry(variant_dict=variant_dict) == test_value
def test_dict_two_separators_with_key(): """Test to get the raw chromosome""" variant_dict = get_variant_dict(info="RankScore=1:12,2:11") variant_line = get_variant_line(info="RankScore=1:12,2:11") plugin = Plugin( name='rank_score', field='INFO', info_key="RankScore", separators=[',', ':'], dict_entry=True ) dict_entry = plugin.get_raw_entry( variant_dict=variant_dict, dict_key='1' ) line_entry = plugin.get_raw_entry( variant_line=variant_line, dict_key='1' ) assert dict_entry == '12' assert line_entry == '12'
def test_dict_three_separators_with_key(): """Test to get the raw chromosome""" variant_dict = get_variant_dict(info="GeneticModels=1:AD|AD_dn,2:AR_hom") variant_line = get_variant_line(info="GeneticModels=1:AD|AD_dn,2:AR_hom") plugin = Plugin( name='genetic_models', field='INFO', info_key="GeneticModels", separators=[',', ':', '|'], dict_entry=True ) dict_entry = plugin.get_raw_entry( variant_dict=variant_dict, dict_key='1' ) line_entry = plugin.get_raw_entry( variant_line=variant_line, dict_key='1' ) assert dict_entry == 'AD|AD_dn' assert line_entry == 'AD|AD_dn'
def test_gt_call_no_header_dict(): """Test to get the raw chromosome""" plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT') variant_dict = get_variant_dict() assert plugin.get_raw_entry(variant_dict=variant_dict, individual_id='ADM1003A3') == '1/1'