Question

Extracting matching lines using perl is known to me but I want the lines from two files which are not matching i.e. they are unique to the file among two text files.

file1:

one|E2027.1|073467|66   ATGCTATGTTTTGCTAAT  
one|E2002.1|073405|649  ATGAAAGCTTTAAAGAAA  
one|E2001.1|734704|201  ATGTTTTCAGGTATTATA  
one|E2025.1|073468|204  ATGAAACAGAAATATATT  
one|E2028.1|073431|578  ATGTTATTTAATTATGGT  
one|E2040.1|073743|862  ATGATTTATCCTAATAAT   

………~2000 such lines

file2:

one|E2027.1|073467|66  
one|E5005.5|000005|005  
one|E2001.1|734704|201  
one|E2025.1|073468|204  
one|E2028.1|073431|578  
one|E2040.1|073743|862    

………~2000 such lines

how to extract the lines not matching using perl or cmd commands?
here e.g. line 2 of file two is unique to file 2…..!!!

Here’s what I have so far

foreach(@2) {
    @org=split('\t',$_);
    chomp($two=$_);
    foreach(@1) {
        if($_=~m/^$two.+/) {
            print OUT1 "$_";
        } else {
            print OUT2 "$_";
        }
    }
}

but else output gives GB of data.

Answer 1

You have to read in one of the files first. Then you can match against the content of each line of the other file. I used first from List::Util to do that. grep is fine, too, but first stops after it finds the first occurrence, which saves you time with large files.

use strict;
use warnings;
use List::Util qw(first);
use 5.014;

my $file1 = <<"FILE1";
one|E2027.1|073467|66\tATGCTATGTTTTGCTAAT
one|E2002.1|073405|649\tATGAAAGCTTTAAAGAAA
one|E2001.1|734704|201\tATGTTTTCAGGTATTATA
one|E2025.1|073468|204\tATGAAACAGAAATATATT
one|E2028.1|073431|578\tATGTTATTTAATTATGGT
one|E2040.1|073743|862\tATGATTTATCCTAATAAT
FILE1

my $file2 = <<"FILE2";
one|E2027.1|073467|66
one|E5005.5|000005|005
one|E2001.1|734704|201
one|E2025.1|073468|204
one|E2028.1|073431|578
one|E2040.1|073743|862
FILE2

my @file1_content = map { (split(/\t/))[0] } split /\n/, $file1;

foreach my $line (split /\n/, $file2) {
  chomp $line; # we need that because the split above is just a filler
  next if first { $_ eq $line } @file1_content;
  say $line;
}

---

I strongly suggest you use strict and warnings in all your programs. They both help you to find small, subtle mistakes. It’s also a good idea to name your variables in a more descriptive way. Arrays named @1 and @2 are very bad. I had trouble understanding which variable did what.