基于列匹配组合两个文件 - 其中一个文件列具有多个相同的条目

Question

I would like to match two files based on one column and combine the matching lines. But one of the files ( file1.txt ) has the same entry more than once. As an example:

file1.txt

chr:123 a
chr:123 b
chr:456 a

file2.txt

chr:123 aa
chr:456 bb

I would like to extract the indexes based on the first column.

The final output should look like:

chr:123 a aa
chr:123 b aa
chr:456 a bb

I tried intersect on R but couldn't figure out how to combine matching lines when file1.txt has the same entry more than once. I am using two for loops but the files are very big and it takes lots of time.

Is there a quicker way to do this in perl or R?

Answer 1

Try this:

one <- data.frame(
id=c("chr:123","chr:123","chr:456"),
value=c("a","b","a")
)

two <- data.frame(
id=c("chr:123","chr:456"),
value=c("aa","bb")
)

merge(one,two,by="id",all.x=TRUE)

#result
       id value.x value.y
1 chr:123       a      aa
2 chr:123       b      aa
3 chr:456       a      bb

Answer 2

Here's another option:

use Modern::Perl;

my %file1Hash;

open my $file1, "<file1.txt" or die $!;
do { my ( $key, $value ) = split; push @{ $file1Hash{$key} }, $value }
  for <$file1>;
close $file1;

open my $file2, "<file2.txt" or die $!;
do {
    my ( $key, $value ) = split;
    do { say "$key $_ $value" for @{ $file1Hash{$key} } } if $file1Hash{$key};
  }
  for <$file2>;
close $file2;

Output:

chr:123 a aa
chr:123 b aa
chr:456 a bb