请帮我解析 VCF 文件。我正在粘贴一个真实的例子。
输入:
1 1014143 rs786201005 C T . . RS=786201005;RSPOS=1014143;dbSNPBuildID=144;SSR=0;SAO=1;VP=0x050068000605000002110100;GENEINFO=ISG15:9636;WGT=1;VC=SNV;PM;PMC;NSN;REF;ASP;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014143C>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=147571.0003;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C4015293:616126:ORPHA319563;CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification;CLNREVSTAT=no_criteria;CLNACC=RCV000162196.3
1 1014228 rs1921 G A,C . . RS=1921;RSPOS=1014228;dbSNPBuildID=36;SSR=0;SAO=0;VP=0x050328000a0517053f000100;GENEINFO=ISG15:9636;WGT=1;VC=SNV;PM;PMC;S3D;SLO;NSM;REF;ASP;VLD;G5A;G5;HD;GNO;KGPhase1;KGPhase3;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014228G>A;CLNSRC=.;CLNORIGIN=1;CLNSRCID=.;CLNSIG=2;CLNDSDB=MedGen;CLNDSDBID=CN169374;CLNDBN=not_specified;CLNREVSTAT=single;CLNACC=RCV000455759.1;CAF=0.6611,0.3389,.;COMMON=1
1 1014316 rs672601345 C CG . . RS=672601345;RSPOS=1014319;dbSNPBuildID=142;SSR=0;SAO=1;VP=0x050068001205000002110200;GENEINFO=ISG15:9636;WGT=1;VC=DIV;PM;PMC;NSF;REF;ASP;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014319dupG;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=147571.0002;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C4015293:616126:ORPHA319563;CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification;CLNREVSTAT=no_criteria;CLNACC=RCV000148989.5
1 1014359 rs672601312 G T . . RS=672601312;RSPOS=1014359;dbSNPBuildID=142;SSR=0;SAO=1;VP=0x050068000605000002110100;GENEINFO=ISG15:9636;WGT=1;VC=SNV;PM;PMC;NSN;REF;ASP;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.11:g.1014359G>T;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=147571.0001;CLNSIG=5;CLNDSDB=MedGen:OMIM:Orphanet;CLNDSDBID=C4015293:616126:ORPHA319563;CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification;CLNREVSTAT=no_criteria;CLNACC=RCV000148988.5
1 1020183 rs539283387 G C . . RS=539283387;RSPOS=1020183;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000a05040026000100;GENEINFO=AGRN:375790;WGT=1;VC=SNV;NSM;REF;ASP;VLD;KGPhase3;CLNALLE=1;CLNHGVS=NC_000001.11:g.1020183G>C;CLNSRC=.;CLNORIGIN=1;CLNSRCID=.;CLNSIG=3;CLNDSDB=MedGen;CLNDSDBID=CN169374;CLNDBN=not_specified;CLNREVSTAT=single;CLNACC=RCV000424799.1;CAF=0.9904,0.009585;COMMON=1
1 1020216 rs764659938 C G . . RS=764659938;RSPOS=1020216;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000a05040002000100;GENEINFO=AGRN:375790;WGT=1;VC=SNV;NSM;REF;ASP;VLD;CLNALLE=1;CLNHGVS=NC_000001.11:g.1020216C>G;CLNSRC=.;CLNORIGIN=1;CLNSRCID=.;CLNSIG=0;CLNDSDB=MedGen;CLNDSDBID=CN221809;CLNDBN=cancer;CLNREVSTAT=single;CLNACC=RCV000422793.1
我需要一个输出:
1014143 rs786201005 C T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014228 rs1921 G A,C CLNSIG=2 CLNDBN=not_specified
1014316 rs672601345 C CG CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014359 rs672601312 G T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1020183 rs539283387 G C CLNSIG=3 CLNDBN=not_specified
1020216 rs764659938 C G CLNSIG=0 CLNDBN=not_provided
这意味着打印列 2,3,4,5 ,然后解析最后一列并打印 CLNSIG 和 CLNDBN 。问题是,这些值并不总是在同一个位置。
我的尝试是:
awk -v OFS="\t"'{print $2,$3,$4,$5,$8}' input
...然后我不知道如何获得 CLNSIG 和 CLNDBN 。
感谢您的任何想法。
答案 0 :(得分:3)
Pure bash
,通过使用bash
来解析剩余的变量
在$h
中, parameter tranformation 输出:
while read a b c d e f g h ; do
declare ${h//;/ }
printf "%s\t%-10s\t%s\t%s\t%s\t%s\n" $b $c $d $e ${CLNSIG@A} ${CLNDBN@A}
done < input
输出:
1014143 rs786201005 C T CLNSIG='5' CLNDBN='Immunodeficiency_38_with_basal_ganglia_calcification'
1014228 rs1921 G A,C CLNSIG='2' CLNDBN='not_specified'
1014316 rs672601345 C CG CLNSIG='5' CLNDBN='Immunodeficiency_38_with_basal_ganglia_calcification'
1014359 rs672601312 G T CLNSIG='5' CLNDBN='Immunodeficiency_38_with_basal_ganglia_calcification'
1020183 rs539283387 G C CLNSIG='3' CLNDBN='not_specified'
1020216 rs764659938 C G CLNSIG='0' CLNDBN='cancer'
POSIX shell,grep
和printf
方法:
while read a b c d e f g h ; do
printf "%s\t%-10s\t%s\t%s\t%s\t%s\n" $b $c $d $e \
$( echo "$h" | grep -o 'CLN\(SIG\|DBN\)=[^;]*' ) ;
done < input
输出:
1014143 rs786201005 C T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014228 rs1921 G A,C CLNSIG=2 CLNDBN=not_specified
1014316 rs672601345 C CG CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014359 rs672601312 G T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1020183 rs539283387 G C CLNSIG=3 CLNDBN=not_specified
1020216 rs764659938 C G CLNSIG=0 CLNDBN=cancer
答案 1 :(得分:2)
使用perl
$ perl -lane 'print join "\t",(@F[1..4], /(?:CLNSIG|CLNDBN)=[^;]+/g)' ip.txt
1014143 rs786201005 C T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014228 rs1921 G A,C CLNSIG=2 CLNDBN=not_specified
1014316 rs672601345 C CG CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1014359 rs672601312 G T CLNSIG=5 CLNDBN=Immunodeficiency_38_with_basal_ganglia_calcification
1020183 rs539283387 G C CLNSIG=3 CLNDBN=not_specified
1020216 rs764659938 C G CLNSIG=0 CLNDBN=cancer
-a
选项可将输入分割为空格,保存在@F
数组/(?:CLNSIG|CLNDBN)=[^;]+/g
将返回CLNSIG
和CLNDBN
字段@F[1..4]
提供第2到第5个字段(索引从0
开始)-lane
选项答案 2 :(得分:2)
可以使用awk完成:
<强> script.awk 强>
BEGIN { OFS="\t" }
{ clnsig = clndbn = ""
if( match( $8, /CLNSIG=[^;]+/ ) ) {
clnsig = substr( $8, RSTART, RLENGTH )
}
if( match( $8, /CLNDBN=[^;]+/ ) ) {
clndbn = substr( $8, RSTART, RLENGTH )
}
print $2, $3, $4, $5, clnsig, clndbn
}
或者更紧凑,以防CLNDBN
之后CLNSIG
总是:
<强> script.awk 强>
BEGIN { OFS="\t" }
{ match($8,/(CLNSIG=[^;]+).*(CLNDBN=[^;]+)/, tmp)
print $2,$3,$4,$5, tmp[1], tmp[2]
}
函数match
匹配正则表达式。第一个表单设置变量RSTART
和RLENGTH
,以便您可以使用substring
提取文本。
第二种形式将数组tmp
中的第一个子表达式(第一个括号)放在位置1,将第二个子表达放置在位置2,依此类推。
正则表达式CLNSIG=[^;]+
匹配文字CLNSIG=
,后跟一个子字符串,但不包括;
。