Question

我有两个文件，我正在尝试根据第1列和第2列加入/合并。

INPUT1

22  42960000    rs149201999 A   AC  100 PASS    LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06

输入2

22  42960000    .   A   AC  .   .    ;AA=1;AFE=0.989691;ASNE=1;EUN=0.992509;AFW=1;MED=0.991071;LAT=1

输出

22  42960000    .   A   AC  .   .    ;AA=1;AFE=0.989691;ASNE=1;EUN=0.992509;AFW=1;MED=0.991071;LAT=1;LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06

注意每个列由制表符分隔。

Answer 1

这应该有效：

s=%%%%%%
join -j1 -o1.1,1.2,1.3,1.4,1.5,1.6,1.7,2.7 <(sed "s/\t/$s/" input2) \
                                           <(sed "s/\t/$s/" input1) \
| sed "s/$s/\t/;
       s/\(=[^ ]*\) \([^ ]*=\)/\1;\2/;
       s/ \+/\t/g"

Answer 2

这是使用GNU awk的一种方式：

awk 'FNR==NR { array[$1,$2]=$8; next } ($1,$2) in array { print $0 ";" array[$1,$2] }' input1 input2

结果：

22  42960000    .   A   AC  .   .    ;AA=1;AFE=0.989691;ASNE=1;EUN=0.992509;AFW=1;MED=0.991071;LAT=1;LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06

根据条件合并/连接

2 个答案: