将一个列表与另一个列表匹配 [英] match one list to another

问题描述

我有一个 txt 文件，其中的数据看起来像这样(测试):

I have a txt file with data that looks like this (TEST):

chr1_10524
chr1_10525
chr1_10562
chr1_8383722
chr1_201327234
chr2_123123

另一个 txt 文件的数据看起来像这样(数据库):

And another txt file with data that looks like this (DATABASE):

chrom chromStart chromEnd name
chr1 67071812 67170812 13_Heterochrom/lo
chr1 201326377 201330777 13_Heterochrom/lo
chr1 8383613 8389213 12_Repressed
chr2 120000 130000 1_Active Promoter

我希望获得一个输出文件，其中 TEST 与 DATABASE 匹配，给出如下内容:

I wish to obtain an output file where the TEST is matched with DATABASE giving something like this:

chr1_8383722 12_Repressed
chr1_201327234 13_Heterochrom/lo
chr2_123123 1_Active Promoter

这可以在 perl 上完成吗?谢谢！

Can this be done on perl? Thank you!

推荐答案

试试这个:

#!/usr/bin/perl

use warnings;
use strict;

open(my $db, "<", "database.txt") or die "Cannot open < database.txt: $!";
open(my $tst, "<", "test.txt") or die "Cannot open < test.txt: $!";

my @database;

while (<$db>) {
    chomp;
    my @fields = split;
    push @database, \@fields;
}

while (my $line = <$tst>) {
    chomp($line);
    my ($chr, $pos) = split /_/, $line;
    # There is not unique key can be used to detect whether an entry is exist
    # in the database.
    foreach my $entry (@database) {
        if ($chr eq $entry->[0] && $entry->[1] <= $pos && $pos <= $entry->[2]) {
            print "$line $entry->[3]\n";
        }
    }
}

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