我想匹配来自两个不同文件的多个列，新输出是file1中的所有列连接在一起，匹配来自文件2或返回＆＃39; null＆＃39;如果他们不匹配。文件未分类。这两个文件都是巨大的并且以制表符分隔。
file1 :(我这里只显示几列，有50多列）
chromosome position reference alternate +50 other columns
1 69511 A G other columns
1 69897 G C other columns
file2是一个数据库文件（（8列）：
#CHROM POS ID REF ALT QUAL FILTER INFO
1 69511 rs75062661 A G 120729371.20 PASS AC=66446;AC_AFR=3767;AC_AMR=5986;AC_Adj=63799;AC_EAS=7618;AC_FIN=3289;AC_Het=1539;AC_Hom=31130;AC_NFE=30553;AC_OTH=437;AC_SAS=12149;AF=0.894;AN=74318;AN_AFR=6394;AN_AMR=6286;AN_Adj=67892;AN_EAS=7622;AN_FIN=3320;AN_NFE=31460;AN_OTH=452;AN_SAS=12358;BaseQRankSum=0.831;ClippingRankSum=1.06;DB;DP=2687838;FS=23.500;GQ_MEAN=224.54;GQ_STDDEV=255.92;Het_AFR=873;Het_AMR=152;Het_EAS=4;Het_FIN=11;Het_NFE=377;Het_OTH=9;Het_SAS=113;Hom_AFR=1447;Hom_AMR=2917;Hom_EAS=3807;Hom_FIN=1639;Hom_NFE=15088;Hom_OTH=214;Hom_SAS=6018;InbreedingCoeff=0.6382;MQ=31.34;MQ0=0;MQRankSum=-4.020e-01;NCC=29303;QD=26.34;ReadPosRankSum=-1.106e+00;VQSLOD=131.28;culprit=FS;DP_HIST=2375|696|240|284|1521|1069|1274|1579|2061|2600|2780|2580|2302|1874|1363|1096|905|839|814|8907,855|552|218|280|521|865|1246|1574|2056|2596|2775|2575|2300|1873|1362|1094|904|839|814|8871;GQ_HIST=945|1293|469|252|189|82|120|127|109|147|156|181|1403|374|268|384|433|374|482|29371,66|523|454|240|147|77|117|126|106|143|156|175|237|309|261|377|432|374|482|29368;CSQ=G|ENSG00000186092|ENST00000335137|Transcript|missense_variant|421|421|141|T/A|Aca/Gca|rs75062661|1||1|OR4F5|HGNC|14825|protein_coding|YES|CCDS30547.1|ENSP00000334393|OR4F5_HUMAN||UPI0000041BC1|tolerated(0.63)|benign(0.003)|1/1||Transmembrane_helices:Tmhmm&Pfam_domain:PF00001&Pfam_domain:PF10320&PROSITE_profiles:PS50262&Superfamily_domains:SSF81321|ENST00000335137.3:c.421A>G|ENSP00000334393.3:p.Thr141Ala|A:0.3480|G:0.33|G:0.65|G:0.87|G:0.70|G:0.544101|G:0.887429|||||||||||
期望的输出：
chromosome position reference alternate +50 other columns from file1 #CHROM POS ID REF ALT QUAL FILTER INFO
1 69511 A G other columns 1 69511 rs75062661 A G 120729371.20 PASS AC=66446;AC_AFR=3767;AC_AMR=5986;AC_Adj=63799;AC_EAS=7618;AC_FIN=3289;AC_Het=1539;AC_Hom=31130;AC_NFE=30553;AC_OTH=437;AC_SAS=12149;AF=0.894;AN=74318;AN_AFR=6394;AN_AMR=6286;AN_Adj=67892;AN_EAS=7622;AN_FIN=3320;AN_NFE=31460;AN_OTH=452;AN_SAS=12358;BaseQRankSum=0.831;ClippingRankSum=1.06;DB;DP=2687838;FS=23.500;GQ_MEAN=224.54;GQ_STDDEV=255.92;Het_AFR=873;Het_AMR=152;Het_EAS=4;Het_FIN=11;Het_NFE=377;Het_OTH=9;Het_SAS=113;Hom_AFR=1447;Hom_AMR=2917;Hom_EAS=3807;Hom_FIN=1639;Hom_NFE=15088;Hom_OTH=214;Hom_SAS=6018;InbreedingCoeff=0.6382;MQ=31.34;MQ0=0;MQRankSum=-4.020e-01;NCC=29303;QD=26.34;ReadPosRankSum=-1.106e+00;VQSLOD=131.28;culprit=FS;DP_HIST=2375|696|240|284|1521|1069|1274|1579|2061|2600|2780|2580|2302|1874|1363|1096|905|839|814|8907,855|552|218|280|521|865|1246|1574|2056|2596|2775|2575|2300|1873|1362|1094|904|839|814|8871;GQ_HIST=945|1293|469|252|189|82|120|127|109|147|156|181|1403|374|268|384|433|374|482|29371,66|523|454|240|147|77|117|126|106|143|156|175|237|309|261|377|432|374|482|29368;CSQ=G|ENSG00000186092|ENST00000335137|Transcript|missense_variant|421|421|141|T/A|Aca/Gca|rs75062661|1||1|OR4F5|HGNC|14825|protein_coding|YES|CCDS30547.1|ENSP00000334393|OR4F5_HUMAN||UPI0000041BC1|tolerated(0.63)|benign(0.003)|1/1||Transmembrane_helices:Tmhmm&Pfam_domain:PF00001&Pfam_domain:PF10320&PROSITE_profiles:PS50262&Superfamily_domains:SSF81321|ENST00000335137.3:c.421A>G|ENSP00000334393.3:p.Thr141Ala|A:0.3480|G:0.33|G:0.65|G:0.87|G:0.70|G:0.544101|G:0.887429|||||||||||
1 69897 G C other columns null null null null null null null null
文件未分类
这个命令只能给我来自file2的匹配行
awk -F '\t' 'NR==FNR{c[$1$2$3$4]++;next};c[$1$2$4$5]>0' file1 file2
我在这个forumn中找到了join命令，但是这个命令输入了所有列来打印file1中的所有列。我有50多列，因此键入所有列是不实际的，容易出错。
答案 0 :(得分：1)
$ cat tst.awk
BEGIN { FS=OFS="\t" }
NR==FNR {
if (FNR==1) {
hdr = $0
gsub(/[^\t]+/,"null")
nulls = $0
}
else {
map[$1,$2,$4,$5] = $0
}
next
}
{
if ( FNR==1 ) {
tail = hdr
}
else if ( ($1,$2,$3,$4) in map ) {
tail = map[$1,$2,$3,$4]
}
else {
tail = nulls
}
print $0, tail
}
$ awk -f tst.awk file2 file1
chromosome position reference alternate +50 other columns #CHROM POS ID REF ALTQUAL FILTER INFO
1 69511 A G other columns 1 69511 rs75062661 A G 120729371.20 PASS AC=66446;AC_AFR=3767;AC_AMR=5986;AC_Adj=63799;AC_EAS=7618;AC_FIN=3289;AC_Het=1539;AC_Hom=31130;AC_NFE=30553;AC_OTH=437;AC_SAS=12149;AF=0.894;AN=74318;AN_AFR=6394;AN_AMR=6286;AN_Adj=67892;AN_EAS=7622;AN_FIN=3320;AN_NFE=31460;AN_OTH=452;AN_SAS=12358;BaseQRankSum=0.831;ClippingRankSum=1.06;DB;DP=2687838;FS=23.500;GQ_MEAN=224.54;GQ_STDDEV=255.92;Het_AFR=873;Het_AMR=152;Het_EAS=4;Het_FIN=11;Het_NFE=377;Het_OTH=9;Het_SAS=113;Hom_AFR=1447;Hom_AMR=2917;Hom_EAS=3807;Hom_FIN=1639;Hom_NFE=15088;Hom_OTH=214;Hom_SAS=6018;InbreedingCoeff=0.6382;MQ=31.34;MQ0=0;MQRankSum=-4.020e-01;NCC=29303;QD=26.34;ReadPosRankSum=-1.106e+00;VQSLOD=131.28;culprit=FS;DP_HIST=2375|696|240|284|1521|1069|1274|1579|2061|2600|2780|2580|2302|1874|1363|1096|905|839|814|8907,855|552|218|280|521|865|1246|1574|2056|2596|2775|2575|2300|1873|1362|1094|904|839|814|8871;GQ_HIST=945|1293|469|252|189|82|120|127|109|147|156|181|1403|374|268|384|433|374|482|29371,66|523|454|240|147|77|117|126|106|143|156|175|237|309|261|377|432|374|482|29368;CSQ=G|ENSG00000186092|ENST00000335137|Transcript|missense_variant|421|421|141|T/A|Aca/Gca|rs75062661|1||1|OR4F5|HGNC|14825|protein_coding|YES|CCDS30547.1|ENSP00000334393|OR4F5_HUMAN||UPI0000041BC1|tolerated(0.63)|benign(0.003)|1/1||Transmembrane_helices:Tmhmm&Pfam_domain:PF00001&Pfam_domain:PF10320&PROSITE_profiles:PS50262&Superfamily_domains:SSF81321|ENST00000335137.3:c.421A>G|ENSP00000334393.3:p.Thr141Ala|A:0.3480|G:0.33|G:0.65|G:0.87|G:0.70|G:0.544101|G:0.887429|||||||||||
1 69897 G C other columns null null null null null null null null
答案 1 :(得分：1)
对于join，不需要输入所有50列+，让一些代码输入。假设join的{{1}}选项需要从文件＃2打印60列。
这是制作重复字符串的一种方法：
-o输出（略有缩写）：
seq -s, 2.01 .01 2.60 | sed 's/\.0/./g'
要使用代码，请将其括在 2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11,2.12, ... 2.58,2.59,2.60
中，（或将其分配给变量），然后使用join：
$()