查找图案并打印下一列(两个文件)

Question

我想在 File2 中查找 File1 第 1 列的模式，然后在 File2 旁边打印 File1 的第二列：

文件1（两列制表符分隔）：

APBW    lung
APCA    non virulent
ABKM    lung
APBX    lung
KK020   -
APBZ    non virulent
AOSU    lung
APBY    non virulent
APBV    joint; lung; CNS
CP001321    virulent
APBT    virulent
APBU    non-virulent
APCB    moderadamente virulenta (nose)
CP005384    -

文件2（两列制表符分隔）：

HS372_00243 gi|219690483|gb|CP001321.1|
HS372_00436 gi|529264994|gb|APBX01000055.1|
HS372_00445 gi|529256455|gb|APBT01000061.1|
HS372_00544 gi|529259149|gb|APBV01000035.1|
HS372_00545 gi|529259149|gb|APBV01000035.1|
HS372_00546 gi|529259149|gb|APBV01000035.1|

所需输出（三列制表符分隔）：

HS372_00243 gi|219690483|gb|CP001321.1| virulent
HS372_00436 gi|529264994|gb|APBX01000055.1| lung
HS372_00445 gi|529256455|gb|APBT01000061.1| virulent
HS372_00544 gi|529259149|gb|APBV01000035.1| jointlungCNS
HS372_00545 gi|529259149|gb|APBV01000035.1| jointlungCNS
HS372_00546 gi|529259149|gb|APBV01000035.1| jointlungCNS

临时 bash 代码（不起作用），但对其他语言开放：

while read vl; do grep "$vl" File2 ; done < File1

也尝试使用 awk（不起作用，因为它似乎正在寻找完全匹配，并且我在 File2 中的字符串被其他东西包围）：

awk 'BEGIN { FS = OFS = "t" } FNR==NR{a[$1]=$0;next}($1 in a){print a[$1],$2,$3}' File1 File2

谢谢，贝尔纳多

Answer 1

像这样的东西听起来像是你想要的：

awk '
BEGIN { FS=OFS="t" }
NR==FNR { map[$1] = $2; next }
{
    for (key in map)
        if ($0 ~ key)
            $0 = $0 OFS map[key]
    print
}
' file1 file2

Answer 2

希望这对你有帮助

file2_contents = [i.strip() for i in open("file2.txt").readlines()]
with open("file1.txt") as file1:
    for each_line in file1.readlines():
        code=each_line.split('t')[0].strip()
        part=each_line.split('t')[1].strip()
        for each_file2_contents in file2_contents:
            if code in each_file2_contents:
                print  each_file2_contents+'t'+part

Answer 3

在 Perl 中：

use warnings;
use strict;
use Data::Dumper;
my $str1 = <<"EOS1";
APBW    lung
APCA    non virulent
ABKM    lung
APBX    lung
KK020   -
APBZ    non virulent
AOSU    lung
APBY    non virulent
APBV    joint; lung; CNS
CP001321    virulent
APBT    virulent
APBU    non-virulent
APCB    moderadamente virulenta (nose)
CP005384    -
EOS1
my $str2 = <<"EOS2";
HS372_00243 gi|219690483|gb|CP001321.1|
HS372_00436 gi|529264994|gb|APBX01000055.1|
HS372_00445 gi|529256455|gb|APBT01000061.1|
HS372_00544 gi|529259149|gb|APBV01000035.1|
HS372_00545 gi|529259149|gb|APBV01000035.1|
HS372_00546 gi|529259149|gb|APBV01000035.1|
EOS2
#HS372_00243 gi|219690483|gb|CP001321.1| virulent
my %data1;my %data2;
foreach my $line ( split(/n+/,$str1) ){
    my @f = split(/t/,$line);
    $data1{$f[0]} = $f[1];
}
my @data2 = split(/n+/,$str2);
foreach my $line ( split(/n+/,$str2) ){
    my @f  = split(/t/,$line);
    my @sf = split(/|/,$f[1]);
    $data2{$sf[3]} = $line;
}
#print Dumper(%data2);
foreach my $s1 ( sort { length($b) <=> length($a) } keys %data1){
    foreach my $d2 (@data2){
        my @f  = split(/t/,$d2);
        my @sf = split(/|/,$f[1]);
        if ($sf[3] =~ m!^$s1!is){
            #warn "found $s1 in $d2n";
            print "$d2t$data1{$s1}n";
        }
    }
}
output:
HS372_00243     gi|219690483|gb|CP001321.1|     virulent
HS372_00445     gi|529256455|gb|APBT01000061.1| virulent
HS372_00544     gi|529259149|gb|APBV01000035.1| joint; lung; CNS
HS372_00545     gi|529259149|gb|APBV01000035.1| joint; lung; CNS
HS372_00546     gi|529259149|gb|APBV01000035.1| joint; lung; CNS
HS372_00436     gi|529264994|gb|APBX01000055.1| lung