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Merge pull request #97 from martijnvermaat/no-format

Write files without FORMAT and genotypes (#95)
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commit ac099c04574c7e7a423c2f04a3a07d33abdee319 2 parents 1dbe5b5 + 9d7f44f
James Casbon authored
View
2  vcf/model.py
@@ -133,7 +133,7 @@ def __init__(self, CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT,
self.alleles = [self.REF]
self.alleles.extend(self.ALT)
#: list of ``_Calls`` for each sample ordered as in source VCF
- self.samples = samples
+ self.samples = samples or []
self._sample_indexes = sample_indexes
def __eq__(self, other):
View
13 vcf/parser.py
@@ -220,6 +220,7 @@ def __init__(self, fsock=None, filename=None, compressed=False, prepend_chr=Fals
self.samples = None
self._sample_indexes = None
self._header_lines = []
+ self._column_headers = []
self._tabix = None
self._prepend_chr = prepend_chr
self._parse_metainfo()
@@ -274,7 +275,8 @@ def _parse_metainfo(self):
line = self.reader.next()
- fields = re.split('\t| +', line)
+ fields = re.split('\t| +', line[1:])
+ self._column_headers = fields[:9]
self.samples = fields[9:]
self._sample_indexes = dict([(x,i) for (i,x) in enumerate(self.samples)])
@@ -538,8 +540,6 @@ def fetch(self, chrom, start, end=None):
class Writer(object):
""" VCF Writer """
- fixed_fields = "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT".split()
-
# Reverse keys and values in header field count dictionary
counts = dict((v,k) for k,v in field_counts.iteritems())
@@ -574,13 +574,16 @@ def __init__(self, stream, template, lineterminator="\r\n"):
def _write_header(self):
# TODO: write INFO, etc
- self.writer.writerow(self.fixed_fields + self.template.samples)
+ self.stream.write('#' + '\t'.join(self.template._column_headers
+ + self.template.samples) + '\n')
def write_record(self, record):
""" write a record to the file """
ffs = self._map(str, [record.CHROM, record.POS, record.ID, record.REF]) \
+ [self._format_alt(record.ALT), record.QUAL or '.', self._format_filter(record.FILTER),
- self._format_info(record.INFO), record.FORMAT]
+ self._format_info(record.INFO)]
+ if record.FORMAT:
+ ffs.append(record.FORMAT)
samples = [self._format_sample(record.FORMAT, sample)
for sample in record.samples]
View
200 vcf/test/1kg.sites.vcf
@@ -0,0 +1,200 @@
+##fileformat=VCFv4.1
+##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
+##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
+##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
+##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
+##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
+##ALT=<ID=DEL,Description="Deletion">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
+##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
+##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
+##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
+##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
+##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
+##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
+##reference=GRCh37
+#CHROM POS ID REF ALT QUAL FILTER INFO
+1 10583 rs58108140 G A 100 PASS AVGPOST=0.7707;RSQ=0.4319;LDAF=0.2327;ERATE=0.0161;AN=2184;VT=SNP;AA=.;THETA=0.0046;AC=314;SNPSOURCE=LOWCOV;AF=0.14;ASN_AF=0.13;AMR_AF=0.17;AFR_AF=0.04;EUR_AF=0.21
+1 10611 rs189107123 C G 100 PASS AN=2184;THETA=0.0077;VT=SNP;AA=.;AC=41;ERATE=0.0048;SNPSOURCE=LOWCOV;AVGPOST=0.9330;LDAF=0.0479;RSQ=0.3475;AF=0.02;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.02
+1 13302 rs180734498 C T 100 PASS THETA=0.0048;AN=2184;AC=249;VT=SNP;AA=.;RSQ=0.6281;LDAF=0.1573;SNPSOURCE=LOWCOV;AVGPOST=0.8895;ERATE=0.0058;AF=0.11;ASN_AF=0.02;AMR_AF=0.08;AFR_AF=0.21;EUR_AF=0.14
+1 13327 rs144762171 G C 100 PASS AVGPOST=0.9698;AN=2184;VT=SNP;AA=.;RSQ=0.6482;AC=59;SNPSOURCE=LOWCOV;ERATE=0.0012;LDAF=0.0359;THETA=0.0204;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04
+1 13957 rs201747181 TC T 28 PASS AA=TC;AC=35;AF=0.02;AFR_AF=0.02;AMR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.8711;ERATE=0.0065;EUR_AF=0.02;LDAF=0.0788;RSQ=0.2501;THETA=0.0100;VT=INDEL
+1 13980 rs151276478 T C 100 PASS AN=2184;AC=45;ERATE=0.0034;THETA=0.0139;RSQ=0.3603;LDAF=0.0525;VT=SNP;AA=.;AVGPOST=0.9221;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02
+1 30923 rs140337953 G T 100 PASS AC=1584;AA=T;AN=2184;RSQ=0.5481;VT=SNP;THETA=0.0162;SNPSOURCE=LOWCOV;ERATE=0.0183;LDAF=0.6576;AVGPOST=0.7335;AF=0.73;ASN_AF=0.89;AMR_AF=0.80;AFR_AF=0.48;EUR_AF=0.73
+1 46402 rs199681827 C CTGT 31 PASS AA=.;AC=8;AF=0.0037;AFR_AF=0.01;AN=2184;ASN_AF=0.0017;AVGPOST=0.8325;ERATE=0.0072;LDAF=0.0903;RSQ=0.0960;THETA=0.0121;VT=INDEL
+1 47190 rs200430748 G GA 192 PASS AA=G;AC=29;AF=0.01;AFR_AF=0.06;AMR_AF=0.0028;AN=2184;AVGPOST=0.9041;ERATE=0.0041;LDAF=0.0628;RSQ=0.2883;THETA=0.0153;VT=INDEL
+1 51476 rs187298206 T C 100 PASS ERATE=0.0021;AA=C;AC=18;AN=2184;VT=SNP;THETA=0.0103;LDAF=0.0157;SNPSOURCE=LOWCOV;AVGPOST=0.9819;RSQ=0.5258;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01
+1 51479 rs116400033 T A 100 PASS RSQ=0.7414;AVGPOST=0.9085;AA=T;AN=2184;THETA=0.0131;AC=235;VT=SNP;LDAF=0.1404;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.03;EUR_AF=0.22
+1 51914 rs190452223 T G 100 PASS ERATE=0.0004;AVGPOST=0.9985;THETA=0.0159;AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4089;LDAF=0.0012;AF=0.0005;ASN_AF=0.0017
+1 51935 rs181754315 C T 100 PASS THETA=0.0126;AA=C;AN=2184;RSQ=0.1888;AVGPOST=0.9972;LDAF=0.0015;VT=SNP;AC=0;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0
+1 51954 rs185832753 G C 100 PASS LDAF=0.0021;AA=G;AN=2184;RSQ=0.4692;AVGPOST=0.9975;VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0029;ERATE=0.0006;AC=2;AF=0.0009;AMR_AF=0.01
+1 52058 rs62637813 G C 100 PASS AA=C;ERATE=0.0057;AN=2184;AVGPOST=0.9264;VT=SNP;RSQ=0.4882;AC=64;SNPSOURCE=LOWCOV;LDAF=0.0620;THETA=0.0069;AF=0.03;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.05
+1 52144 rs190291950 T A 100 PASS THETA=0.0093;ERATE=0.0013;LDAF=0.0156;AA=T;AN=2184;VT=SNP;RSQ=0.5220;AVGPOST=0.9811;SNPSOURCE=LOWCOV;AC=21;AF=0.01;ASN_AF=0.0035;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01
+1 52185 rs201374420 TTAA T 244 PASS AA=.;AC=10;AF=0.0046;AFR_AF=0.0020;AMR_AF=0.02;AN=2184;ASN_AF=0.0035;AVGPOST=0.9840;ERATE=0.0037;LDAF=0.0124;RSQ=0.4271;THETA=0.0232;VT=INDEL
+1 52238 rs150021059 T G 100 PASS THETA=0.0132;AA=G;AN=2184;RSQ=0.6256;VT=SNP;ERATE=0.0026;AVGPOST=0.8617;SNPSOURCE=LOWCOV;AC=1941;LDAF=0.8423;AF=0.89;ASN_AF=0.99;AMR_AF=0.93;AFR_AF=0.64;EUR_AF=0.95
+1 53234 rs199502715 CAT C 227 PASS AA=CAT;AC=10;AF=0.0046;AFR_AF=0.02;AMR_AF=0.0028;AN=2184;AVGPOST=0.9936;ERATE=0.0007;LDAF=0.0074;RSQ=0.6237;THETA=0.0119;VT=INDEL
+1 54353 rs140052487 C A 100 PASS THETA=0.0026;AA=C;AN=2184;AC=16;VT=SNP;RSQ=0.5074;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0146;ERATE=0.0058;AF=0.01;ASN_AF=0.01;AMR_AF=0.0028;AFR_AF=0.02;EUR_AF=0.0013
+1 54421 rs146477069 A G 100 PASS ERATE=0.0013;AN=2184;AC=220;VT=SNP;RSQ=0.7869;AVGPOST=0.9461;AA=A;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.1190;AF=0.10;ASN_AF=0.25;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.02
+1 54490 rs141149254 G A 100 PASS ERATE=0.0004;THETA=0.0074;AA=G;AN=2184;VT=SNP;RSQ=0.8366;AVGPOST=0.9646;AC=175;SNPSOURCE=LOWCOV;LDAF=0.0929;AF=0.08;ASN_AF=0.0035;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.15
+1 54676 rs2462492 C T 100 PASS LDAF=0.1528;RSQ=0.6989;AA=T;AN=2184;AC=267;VT=SNP;AVGPOST=0.8998;SNPSOURCE=LOWCOV;THETA=0.0110;ERATE=0.0037;AF=0.12;ASN_AF=0.02;AMR_AF=0.20;AFR_AF=0.09;EUR_AF=0.18
+1 54753 rs143174675 T G 100 PASS AA=T;AN=2184;RSQ=0.6820;AC=65;VT=SNP;THETA=0.0080;ERATE=0.0016;SNPSOURCE=LOWCOV;AVGPOST=0.9697;LDAF=0.0399;AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.03
+1 55164 rs3091274 C A 100 PASS AN=2184;VT=SNP;ERATE=0.0045;AA=A;THETA=0.0162;SNPSOURCE=LOWCOV;AC=1955;RSQ=0.6373;AVGPOST=0.8686;LDAF=0.8489;AF=0.90;ASN_AF=0.99;AMR_AF=0.94;AFR_AF=0.65;EUR_AF=0.96
+1 55249 rs200769871 C CTATGG 443 PASS AA=C;AC=151;AF=0.07;AFR_AF=0.03;AMR_AF=0.08;AN=2184;ASN_AF=0.16;AVGPOST=0.9073;ERATE=0.0063;EUR_AF=0.02;LDAF=0.0968;RSQ=0.5891;THETA=0.0038;VT=INDEL
+1 55299 rs10399749 C T 100 PASS RSQ=0.7602;LDAF=0.2954;AN=2184;VT=SNP;ERATE=0.0051;AA=c;AC=554;SNPSOURCE=LOWCOV;AVGPOST=0.8845;THETA=0.0070;AF=0.25;ASN_AF=0.33;AMR_AF=0.21;AFR_AF=0.39;EUR_AF=0.13
+1 55313 rs182462964 A T 100 PASS ERATE=0.0004;RSQ=0.6112;AVGPOST=0.9994;AN=2184;VT=SNP;THETA=0.0057;AA=A;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020
+1 55326 rs3107975 T C 100 PASS AA=C;ERATE=0.0074;AN=2184;THETA=0.0085;VT=SNP;SNPSOURCE=LOWCOV;AVGPOST=0.9622;AC=90;RSQ=0.6901;LDAF=0.0562;AF=0.04;ASN_AF=0.07;AMR_AF=0.02;AFR_AF=0.07;EUR_AF=0.01
+1 55330 rs185215913 G A 100 PASS ERATE=0.0005;AA=G;AN=2184;VT=SNP;THETA=0.0086;AVGPOST=0.9988;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4701;AF=0.0005;AFR_AF=0.0020
+1 55367 rs190850374 G A 100 PASS ERATE=0.0004;THETA=0.0044;AA=G;AN=2184;VT=SNP;LDAF=0.0029;RSQ=0.3860;SNPSOURCE=LOWCOV;AVGPOST=0.9961;AC=2;AF=0.0009;AMR_AF=0.01
+1 55388 rs182711216 C T 100 PASS THETA=0.0102;ERATE=0.0005;AA=C;AVGPOST=0.9983;AN=2184;LDAF=0.0010;VT=SNP;RSQ=0.2348;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017
+1 55394 rs2949420 T A 100 PASS AC=18;AN=2184;VT=SNP;AA=A;RSQ=0.4995;AVGPOST=0.9784;LDAF=0.0171;SNPSOURCE=LOWCOV;ERATE=0.0012;THETA=0.0063;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02
+1 55416 rs193242050 G A 100 PASS AA=G;AN=2184;AVGPOST=0.9944;VT=SNP;LDAF=0.0064;AC=9;THETA=0.0019;RSQ=0.6553;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0041;AFR_AF=0.02
+1 55427 rs183189405 T C 100 PASS THETA=0.0054;AA=T;AN=2184;VT=SNP;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;RSQ=0.2759;ERATE=0.0007;AF=0.0005;AFR_AF=0.0020
+1 55816 rs187434873 G A 100 PASS AN=2184;THETA=0.0119;VT=SNP;AC=10;RSQ=0.4578;AA=A;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0108;ERATE=0.0007;AF=0.0046;AMR_AF=0.01;EUR_AF=0.01
+1 55850 rs191890754 C G 100 PASS AVGPOST=0.9921;AA=G;AN=2184;VT=SNP;RSQ=0.4083;THETA=0.0045;LDAF=0.0056;AC=5;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0023;EUR_AF=0.01
+1 55852 rs184233019 G C 100 PASS THETA=0.0137;AA=G;AN=2184;RSQ=0.5433;ERATE=0.0009;LDAF=0.0046;VT=SNP;AVGPOST=0.9953;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.01;EUR_AF=0.0013
+1 56644 rs143342222 A C 100 PASS AN=2184;AVGPOST=0.9962;LDAF=0.0040;ERATE=0.0024;VT=SNP;AA=A;RSQ=0.5700;AC=5;SNPSOURCE=LOWCOV;THETA=0.0117;AF=0.0023;AFR_AF=0.01
+1 57952 rs189727433 A C 100 PASS AA=C;ERATE=0.0085;AN=2184;LDAF=0.7878;VT=SNP;THETA=0.0076;RSQ=0.4712;AC=1902;SNPSOURCE=LOWCOV;AVGPOST=0.7578;AF=0.87;ASN_AF=0.98;AMR_AF=0.91;AFR_AF=0.64;EUR_AF=0.91
+1 58814 rs114420996 G A 100 PASS AC=223;THETA=0.0032;AA=G;AN=2184;RSQ=0.9087;LDAF=0.1074;VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0006;AVGPOST=0.9777;AF=0.10;ASN_AF=0.03;AMR_AF=0.17;AFR_AF=0.20;EUR_AF=0.06
+1 59040 rs149755937 T C 100 PASS AVGPOST=0.9710;AC=115;AA=T;AN=2184;RSQ=0.8248;VT=SNP;ERATE=0.0017;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.0613;AF=0.05;ASN_AF=0.03;AMR_AF=0.15;AFR_AF=0.0041;EUR_AF=0.06
+1 60726 rs192328835 C A 100 PASS AVGPOST=0.9092;AN=2184;RSQ=0.5988;ERATE=0.0081;AC=144;VT=SNP;THETA=0.0045;AA=A;SNPSOURCE=LOWCOV;LDAF=0.0959;AF=0.07;ASN_AF=0.05;AMR_AF=0.10;AFR_AF=0.11;EUR_AF=0.03
+1 61442 rs74970982 A G 100 PASS LDAF=0.9152;AA=G;AN=2184;VT=SNP;ERATE=0.0026;RSQ=0.4867;AVGPOST=0.9004;SNPSOURCE=LOWCOV;THETA=0.0013;AC=2084;AF=0.95;ASN_AF=1.00;AMR_AF=0.97;AFR_AF=0.84;EUR_AF=0.99
+1 61462 rs56992750 T A 100 PASS THETA=0.0023;LDAF=0.0378;RSQ=0.7396;AA=T;AN=2184;AVGPOST=0.9773;VT=SNP;AC=68;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.03;AMR_AF=0.02;AFR_AF=0.13
+1 61743 rs184286948 G C 100 PASS AVGPOST=0.9939;LDAF=0.0047;AA=G;AN=2184;VT=SNP;ERATE=0.0011;SNPSOURCE=LOWCOV;AC=4;THETA=0.0016;RSQ=0.4838;AF=0.0018;AMR_AF=0.01;EUR_AF=0.0026
+1 61987 rs76735897 A G 100 PASS THETA=0.0015;AN=2184;AC=569;VT=SNP;AA=A;RSQ=0.7192;AVGPOST=0.8533;LDAF=0.2944;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.26;ASN_AF=0.07;AMR_AF=0.31;AFR_AF=0.25;EUR_AF=0.39
+1 61989 rs77573425 G C 100 PASS RSQ=0.7254;AVGPOST=0.8584;AA=G;AN=2184;LDAF=0.2849;VT=SNP;AC=555;THETA=0.0019;SNPSOURCE=LOWCOV;ERATE=0.0007;AF=0.25;ASN_AF=0.07;AMR_AF=0.31;AFR_AF=0.22;EUR_AF=0.39
+1 61993 rs190553843 C T 100 PASS AC=7;RSQ=0.6106;AA=C;THETA=0.0143;AN=2184;ERATE=0.0009;VT=SNP;AVGPOST=0.9953;SNPSOURCE=LOWCOV;LDAF=0.0050;AF=0.0032;AFR_AF=0.01
+1 62156 rs181864839 C T 100 PASS ERATE=0.0005;AA=C;AN=2184;AVGPOST=0.9979;LDAF=0.0015;VT=SNP;THETA=0.0094;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4561;AF=0.0005;AFR_AF=0.0020
+1 62157 rs10399597 G A 100 PASS AVGPOST=0.9945;AA=G;AN=2184;ERATE=0.0025;VT=SNP;RSQ=0.5217;AC=5;THETA=0.0066;SNPSOURCE=LOWCOV;LDAF=0.0050;AF=0.0023;AFR_AF=0.01
+1 62162 rs140556834 G A 100 PASS AA=G;AN=2184;AC=8;LDAF=0.0057;VT=SNP;THETA=0.0018;ERATE=0.0017;RSQ=0.6089;AVGPOST=0.9948;SNPSOURCE=LOWCOV;AF=0.0037;AMR_AF=0.0028;AFR_AF=0.01;EUR_AF=0.0013
+1 63276 rs185977555 G A 100 PASS RSQ=0.2744;AA=G;AN=2184;AVGPOST=0.9947;VT=SNP;ERATE=0.0010;SNPSOURCE=LOWCOV;AC=1;THETA=0.0010;LDAF=0.0031;AF=0.0005;AFR_AF=0.0020
+1 63297 rs188886746 G A 100 PASS ERATE=0.0005;AVGPOST=0.9986;AA=G;AN=2184;VT=SNP;AC=0;SNPSOURCE=LOWCOV;RSQ=0.2459;THETA=0.0024;LDAF=0.0008;AF=0
+1 63671 rs116440577 G A 100 PASS AA=G;AN=2184;ERATE=0.0047;LDAF=0.1773;VT=SNP;THETA=0.0072;AC=369;SNPSOURCE=LOWCOV;RSQ=0.8980;AVGPOST=0.9652;AF=0.17;ASN_AF=0.05;AMR_AF=0.22;AFR_AF=0.35;EUR_AF=0.11
+1 63735 rs201888535 CCTA C 455 PASS AA=CCTA;AC=829;AF=0.38;AFR_AF=0.13;AMR_AF=0.33;AN=2184;ASN_AF=0.69;AVGPOST=0.7654;ERATE=0.0047;EUR_AF=0.34;LDAF=0.4128;RSQ=0.6424;THETA=0.0062;VT=INDEL
+1 64649 rs181431124 A C 100 PASS RSQ=0.6975;AN=2184;VT=SNP;AA=.;ERATE=0.0008;AVGPOST=0.9918;SNPSOURCE=LOWCOV;AC=21;THETA=0.0024;LDAF=0.0114;AF=0.01;AMR_AF=0.01;EUR_AF=0.03
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+1 88169 rs940550 C T 100 PASS RSQ=0.7811;AN=2184;VT=SNP;AA=.;THETA=0.0055;LDAF=0.2576;ERATE=0.0018;SNPSOURCE=LOWCOV;AC=506;AVGPOST=0.8932;AF=0.23;ASN_AF=0.29;AMR_AF=0.33;AFR_AF=0.33;EUR_AF=0.08
+1 88172 rs940551 G A 100 PASS RSQ=0.7703;AVGPOST=0.9669;LDAF=0.0483;AN=2184;ERATE=0.0009;VT=SNP;AA=.;THETA=0.0027;SNPSOURCE=LOWCOV;AC=86;AF=0.04;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.09
+1 88177 rs143215837 G C 100 PASS ERATE=0.0004;AN=2184;LDAF=0.0456;VT=SNP;AA=.;AVGPOST=0.9686;AC=82;THETA=0.0089;SNPSOURCE=LOWCOV;RSQ=0.7787;AF=0.04;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.09
+1 88188 rs148331237 C A 100 PASS THETA=0.0039;AN=2184;VT=SNP;AA=.;AC=9;LDAF=0.0085;SNPSOURCE=LOWCOV;ERATE=0.0007;RSQ=0.5212;AVGPOST=0.9910;AF=0.0041;AMR_AF=0.0028;EUR_AF=0.01
+1 88236 rs186918018 C T 100 PASS AVGPOST=0.9904;AN=2184;ERATE=0.0031;RSQ=0.5511;VT=SNP;AA=.;THETA=0.0087;LDAF=0.0097;SNPSOURCE=LOWCOV;AC=11;AF=0.01;AMR_AF=0.02;AFR_AF=0.0041;EUR_AF=0.0026
+1 88250 rs191950833 T A 100 PASS LDAF=0.0013;AN=2184;RSQ=0.1387;VT=SNP;AA=.;AC=0;THETA=0.0019;SNPSOURCE=LOWCOV;ERATE=0.0007;AVGPOST=0.9974;AF=0
+1 88316 rs113759966 G A 100 PASS LDAF=0.0531;AN=2184;VT=SNP;AA=.;THETA=0.0071;RSQ=0.7791;AVGPOST=0.9644;ERATE=0.0008;AC=87;SNPSOURCE=LOWCOV;AF=0.04;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.01;EUR_AF=0.09
+1 88324 rs183326616 A G 100 PASS ERATE=0.0004;AN=2184;AVGPOST=0.9996;VT=SNP;AA=.;RSQ=0.7073;LDAF=0.0006;SNPSOURCE=LOWCOV;AC=1;THETA=0.0092;AF=0.0005;AFR_AF=0.0020
+1 88338 rs55700207 G A 100 PASS THETA=0.0035;RSQ=0.7967;AN=2184;ERATE=0.0034;LDAF=0.1019;VT=SNP;AA=.;AC=186;SNPSOURCE=LOWCOV;AVGPOST=0.9507;AF=0.09;ASN_AF=0.03;AMR_AF=0.15;AFR_AF=0.14;EUR_AF=0.05
+1 88370 rs185487977 G A 100 PASS AVGPOST=0.9957;LDAF=0.0035;AN=2184;ERATE=0.0009;RSQ=0.4507;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=4;THETA=0.0043;AF=0.0018;AMR_AF=0.0028;EUR_AF=0.0040
+1 88376 rs189954431 T G 100 PASS RSQ=0.6404;AVGPOST=0.9994;AN=2184;VT=SNP;AA=.;THETA=0.0057;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0003;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020
+1 88388 rs182344336 C T 100 PASS THETA=0.0048;ERATE=0.0005;RSQ=0.3843;AVGPOST=0.9977;LDAF=0.0016;AN=2184;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017
+1 88429 rs146027550 T C 100 PASS LDAF=0.0083;AN=2184;AC=13;RSQ=0.6097;VT=SNP;AA=.;ERATE=0.0010;AVGPOST=0.9922;SNPSOURCE=LOWCOV;THETA=0.0069;AF=0.01;AMR_AF=0.01;AFR_AF=0.02;EUR_AF=0.0013
+1 88710 rs186575039 C G 100 PASS ERATE=0.0005;AC=73;THETA=0.0022;AN=2184;VT=SNP;AA=.;AVGPOST=0.9774;LDAF=0.0389;SNPSOURCE=LOWCOV;RSQ=0.8058;AF=0.03;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.08
+1 89165 rs192631277 A C 100 PASS RSQ=0.2647;AN=2184;ERATE=0.0009;VT=SNP;AA=.;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;THETA=0.0043;AF=0.0005;ASN_AF=0.0017
+1 89744 rs184101761 A G 100 PASS THETA=0.0068;ERATE=0.0004;AVGPOST=0.9985;LDAF=0.0016;AN=2184;RSQ=0.5853;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=2;AF=0.0009;AFR_AF=0.0041
+1 89794 rs188661839 T C 100 PASS AN=2184;THETA=0.0130;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0006;RSQ=0.3812;AVGPOST=0.9984;LDAF=0.0012;AF=0.0005;AFR_AF=0.0020
+1 89946 rs138808727 A T 100 PASS RSQ=0.7414;LDAF=0.1417;AN=2184;ERATE=0.0009;AC=236;VT=SNP;AA=.;THETA=0.0100;AVGPOST=0.9001;SNPSOURCE=LOWCOV;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.02;EUR_AF=0.22
+1 91190 rs143856811 G A 100 PASS AN=2184;AC=77;ERATE=0.0009;VT=SNP;AA=.;LDAF=0.0447;SNPSOURCE=LOWCOV;RSQ=0.7517;THETA=0.0113;AVGPOST=0.9690;AF=0.04;ASN_AF=0.0017;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.08
+1 91228 rs139873689 A G 100 PASS AN=2184;AVGPOST=0.9924;AC=8;RSQ=0.5097;VT=SNP;AA=.;ERATE=0.0010;THETA=0.0012;SNPSOURCE=LOWCOV;LDAF=0.0070;AF=0.0037;AFR_AF=0.02
+1 91536 rs77418980 G T 100 PASS AC=695;AN=2184;ERATE=0.0025;AVGPOST=0.7792;VT=SNP;AA=.;THETA=0.0018;LDAF=0.3255;RSQ=0.6634;SNPSOURCE=LOWCOV;AF=0.32;ASN_AF=0.34;AMR_AF=0.30;AFR_AF=0.04;EUR_AF=0.50
+1 91581 rs151118460 G A 100 PASS AVGPOST=0.7763;THETA=0.0078;AN=2184;VT=SNP;AA=.;AC=716;ERATE=0.0035;LDAF=0.3353;RSQ=0.6618;SNPSOURCE=LOWCOV;AF=0.33;ASN_AF=0.37;AMR_AF=0.30;AFR_AF=0.04;EUR_AF=0.50
+1 91605 rs141083882 C T 100 PASS AC=105;LDAF=0.0597;AN=2184;RSQ=0.7792;VT=SNP;AA=.;ERATE=0.0010;AVGPOST=0.9660;SNPSOURCE=LOWCOV;THETA=0.0070;AF=0.05;AMR_AF=0.02;AFR_AF=0.20
+1 92633 rs149776517 C T 100 PASS THETA=0.0054;AN=2184;VT=SNP;AA=.;AC=44;AVGPOST=0.9592;ERATE=0.0008;LDAF=0.0366;SNPSOURCE=LOWCOV;RSQ=0.5870;AF=0.02;AMR_AF=0.02;EUR_AF=0.05
+1 92858 rs147061536 G T 100 PASS AC=248;THETA=0.0212;RSQ=0.7567;AN=2184;ERATE=0.0046;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AVGPOST=0.9072;LDAF=0.1433;AF=0.11;ASN_AF=0.01;AMR_AF=0.15;AFR_AF=0.05;EUR_AF=0.22
+1 92875 rs193157612 T C 100 PASS THETA=0.0048;AVGPOST=0.9957;AN=2184;LDAF=0.0040;ERATE=0.0009;VT=SNP;AA=.;RSQ=0.4901;SNPSOURCE=LOWCOV;AC=4;AF=0.0018;EUR_AF=0.01
+1 94421 rs200856736 TC T 90 PASS AA=TC;AC=253;AF=0.12;AFR_AF=0.01;AMR_AF=0.20;AN=2184;ASN_AF=0.26;AVGPOST=0.7183;ERATE=0.0117;EUR_AF=0.03;LDAF=0.2244;RSQ=0.3175;THETA=0.0159;VT=INDEL
+1 94986 rs185004859 C T 100 PASS ERATE=0.0166;AN=2184;AC=100;THETA=0.0227;VT=SNP;AA=.;LDAF=0.0872;AVGPOST=0.9040;SNPSOURCE=LOWCOV;RSQ=0.4650;AF=0.05;ASN_AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.04
+1 94991 rs188832636 G A 100 PASS THETA=0.0048;LDAF=0.0041;AN=2184;AVGPOST=0.9944;ERATE=0.0009;VT=SNP;AA=.;SNPSOURCE=LOWCOV;RSQ=0.4157;AC=3;AF=0.0014;AMR_AF=0.0028;EUR_AF=0.0026
+1 98583 rs141344361 T A 100 PASS AVGPOST=0.9463;AC=248;THETA=0.0099;AN=2184;VT=SNP;AA=.;RSQ=0.8090;LDAF=0.1336;ERATE=0.0008;SNPSOURCE=LOWCOV;AF=0.11;ASN_AF=0.30;AMR_AF=0.16;AFR_AF=0.01;EUR_AF=0.02
+1 98929 rs12184306 A G 100 PASS RSQ=0.6226;AVGPOST=0.8784;AN=2184;VT=SNP;AA=.;ERATE=0.0045;LDAF=0.1723;SNPSOURCE=LOWCOV;AC=264;THETA=0.0070;AF=0.12;ASN_AF=0.16;AMR_AF=0.08;AFR_AF=0.16;EUR_AF=0.09
+1 98946 rs191775802 C G 100 PASS AVGPOST=0.9945;ERATE=0.0013;AN=2184;LDAF=0.0046;VT=SNP;AA=.;RSQ=0.4807;SNPSOURCE=LOWCOV;AC=4;THETA=0.0097;AF=0.0018;AFR_AF=0.01
+1 98974 rs12184307 A G 100 PASS AVGPOST=0.8921;AN=2184;AC=224;THETA=0.0130;VT=SNP;AA=.;LDAF=0.1405;RSQ=0.6149;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.10;ASN_AF=0.14;AMR_AF=0.07;AFR_AF=0.14;EUR_AF=0.06
+1 99671 rs146209971 A T 100 PASS THETA=0.0199;AN=2184;AC=13;RSQ=0.4401;VT=SNP;AA=.;ERATE=0.0010;AVGPOST=0.9802;SNPSOURCE=LOWCOV;LDAF=0.0158;AF=0.01;AMR_AF=0.02;AFR_AF=0.0020;EUR_AF=0.01
+1 99687 rs139153227 C T 100 PASS THETA=0.0211;LDAF=0.0470;AN=2184;VT=SNP;AA=.;ERATE=0.0010;RSQ=0.6276;AVGPOST=0.9548;AC=64;SNPSOURCE=LOWCOV;AF=0.03;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.07
+1 99719 rs183898652 C T 100 PASS AN=2184;RSQ=0.5856;VT=SNP;AA=.;AC=10;ERATE=0.0018;SNPSOURCE=LOWCOV;LDAF=0.0076;AVGPOST=0.9925;THETA=0.0251;AF=0.0046;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.0013
+1 100676 rs188226172 A T 100 PASS THETA=0.0212;LDAF=0.0047;AN=2184;VT=SNP;AA=.;RSQ=0.2646;SNPSOURCE=LOWCOV;ERATE=0.0012;AC=2;AVGPOST=0.9925;AF=0.0009;AMR_AF=0.0028;AFR_AF=0.0020
+1 103905 rs142403309 A G 100 PASS AN=2184;THETA=0.0131;ERATE=0.0025;AVGPOST=0.8782;AC=220;VT=SNP;AA=.;LDAF=0.1434;SNPSOURCE=LOWCOV;RSQ=0.5994;AF=0.10;ASN_AF=0.10;AMR_AF=0.14;AFR_AF=0.15;EUR_AF=0.05
+1 106544 rs180741296 C G 100 PASS AC=205;AVGPOST=0.5776;AN=2184;VT=SNP;AA=.;LDAF=0.3120;SNPSOURCE=LOWCOV;ERATE=0.0061;THETA=0.0372;RSQ=0.1442;AF=0.09;ASN_AF=0.11;AMR_AF=0.13;AFR_AF=0.11;EUR_AF=0.05
+1 109107 rs201432136 G GT 67 PASS AA=G;AC=63;AF=0.03;AFR_AF=0.01;AMR_AF=0.04;AN=2184;ASN_AF=0.03;AVGPOST=0.8840;ERATE=0.0122;EUR_AF=0.04;LDAF=0.0890;RSQ=0.3660;THETA=0.0210;VT=INDEL
+1 111513 rs199911222 C CTA 249 PASS AA=.;AC=58;AF=0.03;AFR_AF=0.09;AMR_AF=0.03;AN=2184;ASN_AF=0.0017;AVGPOST=0.9145;ERATE=0.0024;EUR_AF=0.0013;LDAF=0.0665;RSQ=0.4694;THETA=0.0292;VT=INDEL
View
34 vcf/test/test_vcf.py
@@ -192,6 +192,8 @@ class Test1kg(unittest.TestCase):
def testParse(self):
reader = vcf.Reader(fh('1kg.vcf.gz', 'rb'))
+ assert 'FORMAT' in reader._column_headers
+
self.assertEqual(len(reader.samples), 629)
for _ in reader:
pass
@@ -205,6 +207,37 @@ def test_issue_49(self):
pass
+class Test1kgSites(unittest.TestCase):
+
+ def test_reader(self):
+ """The samples attribute should be the empty list."""
+ reader = vcf.Reader(fh('1kg.sites.vcf', 'r'))
+
+ assert 'FORMAT' not in reader._column_headers
+
+ self.assertEqual(reader.samples, [])
+ for record in reader:
+ self.assertEqual(record.samples, [])
+
+ def test_writer(self):
+ """FORMAT should not be written if not present in the template and no
+ extra tab character should be printed if there are no FORMAT fields."""
+ reader = vcf.Reader(fh('1kg.sites.vcf', 'r'))
+ out = StringIO()
+ writer = vcf.Writer(out, reader, lineterminator='\n')
+
+ for record in reader:
+ writer.write_record(record)
+ out.seek(0)
+ out_str = out.getvalue()
+ for line in out_str.split('\n'):
+ if line.startswith('##'):
+ continue
+ if line.startswith('#CHROM'):
+ assert 'FORMAT' not in line
+ assert not line.endswith('\t')
+
+
class TestGatkOutputWriter(unittest.TestCase):
def testWrite(self):
@@ -841,6 +874,7 @@ def test_trim(self):
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestOpenMethods))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestFilter))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(Test1kg))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(Test1kgSites))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestRecord))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestCall))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestRegression))
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