Compare two files

Assuming your files are both sorted:

join -j1 -t\| entity.txt reference.txt 

If they're not sorted, sort them:

sort entity.txt -o entity-sorted.txt sort reference.txt -o reference-sorted.txt join -j1 -t\| entity-sorted.txt reference-sorted.txt 

You can do that with a bash / zsh one-liner. Assuming your data is contained in files named entity and reference, just type:

for i in $(cat entity); do grep ^$i reference; done

in a console.

Also, you can redirect the whole output to an output file, as

for i in $(cat entity); do grep ^$i reference; done > output

A solution using Perl:

Content of entity.txt:

$ cat entity.txt 624197 624252 624264 624276 624280 624309 624317 

Content of reference.txt:

$ cat reference.txt 624252|624346 624264|1070122 624264|624346 624276|624588 624280|624346 624280|624582 624298|624588 624319|333008 624330|624588 

Content of Perl script:

$ cat script.pl use warnings; use strict; ## Check arguments. @ARGV == 2 or die qq[Usage: perl $0 <entity-file> <reference-file>\n]; ## File in process. my $process_file = 1; ## Hash to save entities. my %entity; while ( <> ) { ## Process file of entities. Remove leading and trailing spaces, and save the ## number to a hash. if ( $process_file == 1 ) { s/\A\s*//; s/\s*\z//; if ( defined $_ ) { $entity{ $_ } = 1 } next; } ## Process file of references. Get first field and search it in the hash. ## If found, print the line. my @f = split /\|/, $_, 2; if ( exists $entity{ $f[0] } ) { print; } } continue { ## Increment number when end processing first file. if ( eof ) { ++$process_file } } 

Running the script without arguments:

$ perl script.pl Usage: perl script.pl <entity-file> <reference-file> 

Running the script with arguments and result:

$ perl script.pl entity.txt reference.txt 624252|624346 624264|1070122 624264|624346 624276|624588 624280|624346 624280|624582 

Hmm, maybe I'm missing something? Please correct me if I'm wrong:

$ while read id;do grep $id reference ;done <identity 624252|624346 624264|1070122 624264|624346 624276|624588 624280|624346 624280|624582 

Looking at your source files, they were already sorted, but my solution should work regardless of whether they are sorted or not, I believe.

And to output to another file:

$ while read id;do grep $id reference ;done < identity > newoutput.out