def sname_filter(input_stream, filter_file, output_stream, complement): ''' This reads a VCF stream, determines if the line overlaps any from the filter_file by sname and outputs. ''' filter_list = load_filter_file(filter_file) vcf = Vcf() in_header = True header_lines = list() sample_list = None for line in input_stream: if in_header: header_lines.append(line) if line[0:6] == '#CHROM': in_header = False vcf.add_header(header_lines) vcf.add_info('FOUND', '.', 'String', 'Variant id in other file') output_stream.write(vcf.get_header() + '\n') else: v = Variant(line.rstrip().split('\t'), vcf) sname_set = set_from_string(v.get_info('SNAME')) found = overlapping_ids(sname_set, filter_list) if bool(found) != complement: v.set_info('FOUND', ','.join(found)) output_stream.write(v.get_var_string() + '\n')
def merge_single_bp(BP, sample_order, v_id, use_product, vcf, vcf_out, include_genotypes): A = BP[0].l.rstrip().split('\t') var = Variant(A, vcf) try: sname = var.get_info('SNAME') var.set_info('SNAME', sname + ':' + var.var_id) except KeyError: pass var.var_id = str(v_id) if use_product: var.set_info('ALG', 'PROD') else: var.set_info('ALG', 'SUM') GTS = None if include_genotypes: null_string = null_format_string(A[8]) gt_dict = {sname: A[9]} GTS = '\t'.join([gt_dict.get(x, null_string) for x in sample_order]) var.gts = None var.gts_string = GTS return var
def merge_single_bp(BP, sample_order, v_id, use_product, vcf, vcf_out, include_genotypes): A = BP[0].l.rstrip().split('\t') var = Variant(A,vcf) try: sname = var.get_info('SNAME') var.set_info('SNAME', sname + ':' + var.var_id) except KeyError: pass var.var_id=str(v_id) if use_product: var.set_info('ALG', 'PROD') else: var.set_info('ALG', 'SUM') GTS = None if include_genotypes: null_string = null_format_string(A[8]) gt_dict = { sname: A[9] } GTS = '\t'.join([gt_dict.get(x, null_string) for x in sample_order]) var.gts = None var.gts_string = GTS return var
class TestVariant(TestCase): def setUp(self): header_lines = [ '##fileformat=VCFv4.2', '##fileDate=20151202', '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', '#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878' ] self.vcf = Vcf() self.vcf.add_header(header_lines) self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9' self.variant = Variant(self.variant_line.split('\t'), self.vcf) def test_set_info(self): self.variant.set_info('SVTYPE', 'INV') self.assertEqual(self.variant.info['SVTYPE'], 'INV') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.info['IMAFLAG'], False) with self.assertRaises(SystemExit) as cm: self.variant.set_info('SUPER', True) def test_get_info(self): self.assertEqual(self.variant.get_info('IMAFLAG'), True) self.assertEqual(self.variant.get_info('SVTYPE'), 'BND') with self.assertRaises(KeyError) as cm: self.variant.get_info('CALI') def test_get_info_string(self): self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9;IMAFLAG') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9') def test_get_format_string(self): self.assertEqual(self.variant.get_format_string(), 'GT:SU') def test_genotype(self): self.assertEqual(self.variant.genotype('NA12878').get_gt_string(), '0/0:9') def test_var_string(self): self.assertEqual(self.variant.get_var_string(), self.variant_line)
class TestVariant(TestCase): def setUp(self): header_lines = [ '##fileformat=VCFv4.2', '##fileDate=20151202', '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', '#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA0001' ] self.vcf = Vcf() self.vcf.add_header(header_lines) self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9 1/1:15' self.variant = Variant(self.variant_line.split('\t'), self.vcf) def test_parse_genotypes(self): genotype_field_strings = ['0/1:20', '0/0:15'] parsed_dict = self.variant._parse_genotypes(genotype_field_strings) na12878_gt = Genotype(self.variant, genotype_field_strings[0].split(':')) na0001_gt = Genotype(self.variant, genotype_field_strings[1].split(':')) expected_genotype_dict = {'NA12878': na12878_gt, 'NA0001': na0001_gt} self.assertEqual(parsed_dict, expected_genotype_dict) def test_set_info(self): self.variant.set_info('SVTYPE', 'INV') self.assertEqual(self.variant.info['SVTYPE'], 'INV') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.info['IMAFLAG'], False) with self.assertRaises(SystemExit) as cm: self.variant.set_info('SUPER', True) def test_get_info(self): self.assertEqual(self.variant.get_info('IMAFLAG'), True) self.assertEqual(self.variant.get_info('SVTYPE'), 'BND') with self.assertRaises(KeyError) as cm: self.variant.get_info('CALI') def test_get_info_string(self): self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9;IMAFLAG') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9') def test_get_format_string(self): self.assertEqual(self.variant.get_format_string(), 'GT:SU') def test_get_gt_string(self): self.assertEqual(self.variant.get_gt_string(), '0/0:9 1/1:15') def test_genotype(self): self.assertEqual( self.variant.genotype('NA12878').get_gt_string(), '0/0:9') def test_genotypes(self): self.assertEqual([x.get_gt_string() for x in self.variant.genotypes()], ['0/0:9', '1/1:15']) def test_var_string(self): self.assertEqual(self.variant.get_var_string(), self.variant_line) self.variant.genotype('NA12878').set_format('GT', './.') self.assertEqual( self.variant.get_var_string(use_cached_gt_string=True), self.variant_line) self.assertNotEqual(self.variant.get_var_string(), self.variant_line)
def create_merged_variant(BP, c, v_id, vcf, use_product, weighting_scheme='unweighted'): new_start_L, new_start_R, p_L, p_R, ALG = combine_pdfs( BP, c, use_product, weighting_scheme) max_i_L = p_L.index(max(p_L)) max_i_R = p_R.index(max(p_R)) [cipos95, ciend95] = getCI95(p_L, p_R, max_i_L, max_i_R) new_pos_L = new_start_L + max_i_L new_pos_R = new_start_R + max_i_R BP0 = BP[c[0]] # sometimes after looking at PRs, the left and right can be swapped. # flip them back so downstream tools don't break. if new_pos_R < new_pos_L and BP0.sv_type != 'BND': new_pos_R, new_pos_L = new_pos_L, new_pos_R cipos95, ciend95 = ciend95, cipos95 p_L, p_R = p_R, p_L max_i_R, max_i_L = max_i_L, max_i_R A = BP0.l.rstrip().split('\t', 10) ALT = '' if BP0.sv_type == 'BND': if BP0.strands[:2] == '++': ALT = 'N]' + BP0.right.chrom + ':' + str(new_pos_R) + ']' elif BP0.strands[:2] == '-+': ALT = ']' + BP0.right.chrom + ':' + str(new_pos_R) + ']N' elif BP0.strands[:2] == '+-': ALT = 'N[' + BP0.right.chrom + ':' + str(new_pos_R) + '[' elif BP0.strands[:2] == '--': ALT = '[' + BP0.right.chrom + ':' + str(new_pos_R) + '[N' else: ALT = '<' + BP0.sv_type + '>' var_list = [BP0.left.chrom, new_pos_L, str(v_id), 'N', ALT, 0.0, '.', ''] + A[8:] var = Variant(var_list, vcf) var.set_info('SVTYPE', BP0.sv_type) var.set_info('ALG', ALG) if var.get_info('SVTYPE') == 'DEL': var.set_info('SVLEN', new_pos_L - new_pos_R) elif BP0.left.chrom == BP0.right.chrom: var.set_info('SVLEN', new_pos_R - new_pos_L) else: SVLEN = None if var.get_info('SVTYPE') == 'BND': var.set_info('EVENT', str(v_id)) elif var.get_info('SVTYPE') == 'INS': var.set_info('END', new_pos_L) else: var.set_info('END', new_pos_R) var.set_info('CIPOS95', cipos95) var.set_info('CIEND95', ciend95) var.set_info( 'CIPOS', ','.join([str(x) for x in [-1 * max_i_L, len(p_L) - max_i_L - 1]])) var.set_info( 'CIEND', ','.join([str(x) for x in [-1 * max_i_R, len(p_R) - max_i_R - 1]])) var.set_info('PRPOS', ','.join([str(x) for x in p_L])) var.set_info('PREND', ','.join([str(x) for x in p_R])) return var
class TestVariant(TestCase): def setUp(self): header_lines = [ "##fileformat=VCFv4.2", "##fileDate=20151202", '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA0001", ] self.vcf = Vcf() self.vcf.add_header(header_lines) self.variant_line = ( "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9 1/1:15" ) self.variant = Variant(self.variant_line.split("\t"), self.vcf) def test_parse_genotypes(self): genotype_field_strings = ["0/1:20", "0/0:15"] parsed_dict = self.variant._parse_genotypes(genotype_field_strings) na12878_gt = Genotype(self.variant, genotype_field_strings[0].split(":")) na0001_gt = Genotype(self.variant, genotype_field_strings[1].split(":")) expected_genotype_dict = {"NA12878": na12878_gt, "NA0001": na0001_gt} self.assertEqual(parsed_dict, expected_genotype_dict) def test_set_info(self): self.variant.set_info("SVTYPE", "INV") self.assertEqual(self.variant.info["SVTYPE"], "INV") self.variant.set_info("IMAFLAG", False) self.assertEqual(self.variant.info["IMAFLAG"], False) with self.assertRaises(SystemExit) as cm: self.variant.set_info("SUPER", True) def test_get_info(self): self.assertEqual(self.variant.get_info("IMAFLAG"), True) self.assertEqual(self.variant.get_info("SVTYPE"), "BND") with self.assertRaises(KeyError) as cm: self.variant.get_info("CALI") def test_get_info_string(self): self.assertEqual(self.variant.get_info_string(), "SVTYPE=BND;STRANDS=-+:9;IMAFLAG") self.variant.set_info("IMAFLAG", False) self.assertEqual(self.variant.get_info_string(), "SVTYPE=BND;STRANDS=-+:9") def test_get_format_string(self): self.assertEqual(self.variant.get_format_string(), "GT:SU") def test_get_format_string_caching(self): header_lines = [ "##fileformat=VCFv4.2", "##fileDate=20151202", '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=AS,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878", ] vcf = Vcf() vcf.add_header(header_lines) variant_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:AS:SU 0/0:1:9" variant = Variant(variant_line.split("\t"), vcf) self.assertEqual(variant.get_format_string(), "GT:AS:SU") gts = variant.genotypes() self.assertEqual(variant.get_format_string(), "GT:SU:AS") self.assertEqual(variant.get_format_string(True), "GT:AS:SU") def test_get_gt_string(self): self.assertEqual(self.variant.get_gt_string(), "0/0:9 1/1:15") def test_genotype(self): self.assertEqual(self.variant.genotype("NA12878").get_gt_string(), "0/0:9") def test_set_genotype(self): new_genotype = Genotype(self.variant, ["0/1", "9"]) self.variant.set_genotype("NA12878", new_genotype) self.assertEqual(self.variant.genotype("NA12878").get_gt_string(), "0/1:9") def test_genotypes(self): self.assertEqual([x.get_gt_string() for x in self.variant.genotypes()], ["0/0:9", "1/1:15"]) def test_var_string(self): self.assertEqual(self.variant.get_var_string(), self.variant_line) self.variant.genotype("NA12878").set_format("GT", "./.") self.assertEqual(self.variant.get_var_string(use_cached_gt_string=True), self.variant_line) self.assertNotEqual(self.variant.get_var_string(), self.variant_line) def test_var_string_format_caching(self): header_lines = [ "##fileformat=VCFv4.2", "##fileDate=20151202", '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=AS,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878", ] vcf = Vcf() vcf.add_header(header_lines) variant_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:AS:SU 0/0:1:9" uncached_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU:AS 0/0:9:1" variant = Variant(variant_line.split("\t"), vcf) gt = variant.genotypes() # force parsing self.assertEqual(variant.get_var_string(), uncached_line) self.assertEqual(variant.get_var_string(use_cached_gt_string=True), variant_line) def test_add_genotype(self): header_lines = [ "##fileformat=VCFv4.2", "##fileDate=20151202", '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878", ] vcf = Vcf() vcf.add_header(header_lines) variant_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG SU 9" variant = Variant(variant_line.split("\t"), vcf) self.assertEqual(variant.get_gt_string(), "./.:9")
def run_gt_refine(vcf_in, vcf_out, diag_outfile, gender_file, exclude_file): vcf = Vcf() header = [] in_header = True sex = {} for line in gender_file: v = line.rstrip().split('\t') sex[v[0]] = int(v[1]) exclude = [] if exclude_file is not None: for line in exclude_file: exclude.append(line.rstrip()) outf = open(diag_outfile, 'w', 4096) ct = 1 for line in vcf_in: if in_header: if line[0] == "#": header.append(line) continue else: in_header = False vcf.add_header(header) vcf.add_info('MEDGQR', '1', 'Float', 'Median quality for refined GT') vcf.add_info('Q10GQR', '1', 'Float', 'Q10 quality for refined GT') vcf.add_format('GQR', 1, 'Float', 'Quality of refined genotype.') vcf.add_format('GTR', 1, 'String', 'Refined genotype.') vcf_out.write(vcf.get_header() + '\n') v = line.rstrip().split('\t') info = v[7].split(';') svtype = None for x in info: if x.startswith('SVTYPE='): svtype = x.split('=')[1] break # bail if not DEL or DUP prior to reclassification if svtype not in ['DEL']: vcf_out.write(line) continue var = Variant(v, vcf) sys.stderr.write("%s\n" % var.var_id) sys.stderr.write("%f\n" % float(var.get_info('AF'))) if float(var.get_info('AF')) < 0.01: vcf_out.write(line) else: df = load_df(var, exclude, sex) recdf = recluster(df) if ct == 1: recdf.to_csv(outf, header=True) ct += 1 else: recdf.to_csv(outf, header=False) var.set_info("MEDGQR", '{:.2f}'.format(recdf.iloc[0, :].loc['med_gq_re'])) var.set_info("Q10GQR", '{:.2f}'.format(recdf.iloc[0, :].loc['q10_gq_re'])) recdf.set_index('sample', inplace=True) for s in var.sample_list: if s in recdf.index: var.genotype(s).set_format("GTR", recdf.loc[s, 'GTR']) var.genotype(s).set_format( "GQR", '{:.2f}'.format(recdf.loc[s, 'gq_re'])) else: var.genotype(s).set_format("GTR", "./.") var.genotype(s).set_format("GQR", 0) vcf_out.write( var.get_var_string(use_cached_gt_string=False) + '\n') vcf_out.close() vcf_in.close() gender_file.close() outf.close() if exclude_file is not None: exclude_file.close() return
def run_gt_refine(vcf_in, vcf_out, diag_outfile, gender_file, exclude_file): vcf = Vcf() header = [] in_header = True sex={} for line in gender_file: v = line.rstrip().split('\t') sex[v[0]] = int(v[1]) exclude = [] if exclude_file is not None: for line in exclude_file: exclude.append(line.rstrip()) outf=open(diag_outfile, 'w', 4096) ct=1 for line in vcf_in: if in_header: if line[0] == "#": header.append(line) continue else: in_header = False vcf.add_header(header) vcf.add_info('MEDGQR', '1', 'Float', 'Median quality for refined GT') vcf.add_info('Q10GQR', '1', 'Float', 'Q10 quality for refined GT') vcf.add_format('GQR', 1, 'Float', 'Quality of refined genotype.') vcf.add_format('GTR', 1, 'String', 'Refined genotype.') vcf_out.write(vcf.get_header() + '\n') v = line.rstrip().split('\t') info = v[7].split(';') svtype = None for x in info: if x.startswith('SVTYPE='): svtype = x.split('=')[1] break # bail if not DEL or DUP prior to reclassification if svtype not in ['DEL']: vcf_out.write(line) continue var = Variant(v, vcf) sys.stderr.write("%s\n" % var.var_id) sys.stderr.write("%f\n" % float(var.get_info('AF'))) if float(var.get_info('AF'))<0.01: vcf_out.write(line) else: df=load_df(var, exclude, sex) recdf=recluster(df) if ct==1: recdf.to_csv(outf, header=True) ct += 1 else: recdf.to_csv(outf, header=False) var.set_info("MEDGQR", '{:.2f}'.format(recdf.iloc[0,:].loc['med_gq_re'])) var.set_info("Q10GQR", '{:.2f}'.format(recdf.iloc[0,:].loc['q10_gq_re'])) recdf.set_index('sample', inplace=True) for s in var.sample_list: if s in recdf.index: var.genotype(s).set_format("GTR", recdf.loc[s,'GTR']) var.genotype(s).set_format("GQR", '{:.2f}'.format(recdf.loc[s,'gq_re'])) else: var.genotype(s).set_format("GTR", "./.") var.genotype(s).set_format("GQR", 0) vcf_out.write(var.get_var_string(use_cached_gt_string=False) + '\n') vcf_out.close() vcf_in.close() gender_file.close() outf.close() if exclude_file is not None: exclude_file.close() return
class TestVariant(TestCase): def setUp(self): header_lines = [ '##fileformat=VCFv4.2', '##fileDate=20151202', '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', '#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA0001' ] self.vcf = Vcf() self.vcf.add_header(header_lines) self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9 1/1:15' self.variant = Variant(self.variant_line.split('\t'), self.vcf) def test_parse_genotypes(self): genotype_field_strings = ['0/1:20', '0/0:15'] parsed_dict = self.variant._parse_genotypes(genotype_field_strings) na12878_gt = Genotype(self.variant, genotype_field_strings[0].split(':')) na0001_gt = Genotype(self.variant, genotype_field_strings[1].split(':')) expected_genotype_dict = { 'NA12878': na12878_gt, 'NA0001': na0001_gt } self.assertEqual(parsed_dict, expected_genotype_dict) def test_set_info(self): self.variant.set_info('SVTYPE', 'INV') self.assertEqual(self.variant.info['SVTYPE'], 'INV') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.info['IMAFLAG'], False) with self.assertRaises(SystemExit) as cm: self.variant.set_info('SUPER', True) def test_get_info(self): self.assertEqual(self.variant.get_info('IMAFLAG'), True) self.assertEqual(self.variant.get_info('SVTYPE'), 'BND') with self.assertRaises(KeyError) as cm: self.variant.get_info('CALI') def test_get_info_string(self): self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9;IMAFLAG') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9') def test_get_format_string(self): self.assertEqual(self.variant.get_format_string(), 'GT:SU') def test_get_gt_string(self): self.assertEqual(self.variant.get_gt_string(), '0/0:9 1/1:15') def test_genotype(self): self.assertEqual(self.variant.genotype('NA12878').get_gt_string(), '0/0:9') def test_genotypes(self): self.assertEqual([ x.get_gt_string() for x in self.variant.genotypes() ], ['0/0:9', '1/1:15']) def test_var_string(self): self.assertEqual(self.variant.get_var_string(), self.variant_line) self.variant.genotype('NA12878').set_format('GT', './.') self.assertEqual(self.variant.get_var_string(use_cached_gt_string=True), self.variant_line) self.assertNotEqual(self.variant.get_var_string(), self.variant_line) def test_add_genotype(self): header_lines = [ '##fileformat=VCFv4.2', '##fileDate=20151202', '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', '#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878' ] vcf = Vcf() vcf.add_header(header_lines) variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG SU 9' variant = Variant(variant_line.split('\t'), vcf) self.assertEqual(variant.get_gt_string(), './.:9')
class TestVariant8Col(TestCase): def setUp(self): header_lines = [ '##fileformat=VCFv4.2', '##fileDate=20151202', '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', '#CHROM POS ID REF ALT QUAL FILTER INFO' ] self.vcf = Vcf() self.vcf.add_header(header_lines) self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG' self.variant = Variant(self.variant_line.split('\t'), self.vcf) def test_set_info(self): self.variant.set_info('SVTYPE', 'INV') self.assertEqual(self.variant.info['SVTYPE'], 'INV') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.info['IMAFLAG'], False) with self.assertRaises(SystemExit) as cm: self.variant.set_info('SUPER', True) def test_get_info(self): self.assertEqual(self.variant.get_info('IMAFLAG'), True) self.assertEqual(self.variant.get_info('SVTYPE'), 'BND') with self.assertRaises(KeyError) as cm: self.variant.get_info('CALI') def test_get_info_string(self): self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9;IMAFLAG') self.variant.set_info('IMAFLAG', False) self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9') def test_get_format_string(self): self.assertEqual(self.variant.get_format_string(), None) def test_get_format_string_caching(self): header_lines = [ '##fileformat=VCFv4.2', '##fileDate=20151202', '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">', '##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">', '##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">', '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">', '##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=AS,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">', '##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">', '#CHROM POS ID REF ALT QUAL FILTER INFO' ] vcf = Vcf() vcf.add_header(header_lines) variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG' variant = Variant(variant_line.split('\t'), vcf) self.assertEqual(variant.get_format_string(), None) gts = variant.genotypes() self.assertEqual(variant.get_format_string(), None) self.assertEqual(variant.get_format_string(True), None) def test_get_gt_string(self): self.assertEqual(self.variant.get_gt_string(), None) def test_genotypes(self): self.assertEqual(self.variant.genotypes(), []) def test_var_string(self): self.assertEqual(self.variant.get_var_string(), self.variant_line)
def create_merged_variant(BP, c, v_id, vcf, use_product, weighting_scheme='unweighted'): new_start_L, new_start_R, p_L , p_R, ALG = combine_pdfs(BP, c, use_product, weighting_scheme) max_i_L = p_L.index(max(p_L)) max_i_R = p_R.index(max(p_R)) [cipos95, ciend95]=getCI95( p_L, p_R, max_i_L, max_i_R) new_pos_L = new_start_L + max_i_L new_pos_R = new_start_R + max_i_R BP0=BP[c[0]] A=BP0.l.rstrip().split('\t', 10) ALT = '' if BP0.sv_type == 'BND': if BP0.strands[:2] == '++': ALT = 'N]' + BP0.right.chrom + ':' + str(new_pos_R) + ']' elif BP0.strands[:2] == '-+': ALT = ']' + BP0.right.chrom + ':' + str(new_pos_R) + ']N' elif BP0.strands[:2] == '+-': ALT = 'N[' + BP0.right.chrom + ':' + str(new_pos_R) + '[' elif BP0.strands[:2] == '--': ALT = '[' + BP0.right.chrom + ':' + str(new_pos_R) + '[N' else: ALT = '<' + BP0.sv_type + '>' var_list=[ BP0.left.chrom, new_pos_L, str(v_id), 'N', ALT, 0.0, '.', ''] + A[8:] var=Variant(var_list, vcf) var.set_info('SVTYPE', BP0.sv_type) var.set_info('ALG', ALG) if var.get_info('SVTYPE')=='DEL': var.set_info('SVLEN', new_pos_L - new_pos_R) elif BP0.left.chrom == BP0.right.chrom: var.set_info('SVLEN', new_pos_R - new_pos_L) else: SVLEN = None if var.get_info('SVTYPE') == 'BND': var.set_info('EVENT', str(v_id)) else: var.set_info('END', new_pos_R ) var.set_info('CIPOS95', cipos95) var.set_info('CIEND95', ciend95) var.set_info('CIPOS', ','.join([str(x) for x in [-1*max_i_L, len(p_L) - max_i_L - 1]])) var.set_info('CIEND', ','.join([str(x) for x in [-1*max_i_R, len(p_R) - max_i_R - 1]])) var.set_info('PRPOS', ','.join([str(x) for x in p_L])) var.set_info('PREND', ','.join([str(x) for x in p_R])) return var
def run_gt_refine(vcf_in, vcf_out, diag_outfile, gender_file, exclude_file, batch_file): vcf = Vcf() header = [] in_header = True sex = {} for line in gender_file: v = line.rstrip().split('\t') sex[v[0]] = int(v[1]) exclude = [] if exclude_file is not None: for line in exclude_file: exclude.append(line.rstrip()) batch = dict() if batch_file is not None: for line in batch_file: fields = line.rstrip().split('\t') if fields[1] == 'None': raise RuntimeError('Batch file contains a batch label of None. This label is reserved.') batch[fields[0]] = fields[1] outf = open(diag_outfile, 'w', 4096) ct = 1 for line in vcf_in: if in_header: if line[0] == "#": header.append(line) continue else: in_header = False vcf.add_header(header) vcf.add_info('MEDGQR', '1', 'Float', 'Median quality for refined GT') vcf.add_info('Q10GQR', '1', 'Float', 'Q10 quality for refined GT') vcf.add_format('GQO', 1, 'Integer', 'Quality of original genotype') vcf.add_format('GTO', 1, 'String', 'Genotype before refinement') vcf_out.write(vcf.get_header() + '\n') v = line.rstrip().split('\t') info = v[7].split(';') svtype = None for x in info: if x.startswith('SVTYPE='): svtype = x.split('=')[1] break # bail if not DEL prior to reclassification # DUPs can be quite complicated in their allelic structure # and thus less amenable to refinement by clustering in many cases # INV and BNDs are also unclear. # See earlier commits for code of previous attempts to refine these. if svtype not in ['DEL', 'MEI']: vcf_out.write(line) continue var = Variant(v, vcf) sys.stderr.write("%s\n" % var.var_id) sys.stderr.write("%f\n" % float(var.get_info('AF'))) if float(var.get_info('AF')) < 0.01: vcf_out.write(line) else: df = load_df(var, exclude, sex, batch) recdf = recluster(df) if ct == 1: recdf.to_csv(outf, header=True) ct += 1 else: recdf.to_csv(outf, header=False) var.set_info("MEDGQR", '{:.2f}'.format(recdf.iloc[0, :].loc['med_gq_re'])) var.set_info("Q10GQR", '{:.2f}'.format(recdf.iloc[0, :].loc['q10_gq_re'])) recdf.set_index('sample', inplace=True) for s in var.sample_list: g = var.genotype(s) g.set_format("GTO", g.get_format("GT")) g.set_format("GQO", g.get_format("GQ")) if s in recdf.index: var.genotype(s).set_format("GT", recdf.loc[s, 'GTR']) var.genotype(s).set_format("GQ", '{:.0f}'.format(recdf.loc[s, 'gq_re'])) else: var.genotype(s).set_format("GT", "./.") var.genotype(s).set_format("GQ", 0) vcf_out.write(var.get_var_string(use_cached_gt_string=False) + '\n') vcf_out.close() vcf_in.close() gender_file.close() outf.close() if exclude_file is not None: exclude_file.close() return