Re: Unify two files

This seems to be more or less what you are looking for:

use strict;
use warnings;

my ($mio, $mio2);     

my $filename = '/Users/Pabli/Desktop/do_human_mapping.gmt';
my $match = 'DOID:2055';
unlink ("myoutputfilename3.txt");
unlink ("myoutputfilename4.txt");
open(my $file, '<', $filename) or die "open: $!";

open my $out_file3, '>', 'myoutputfilename3.txt' or die "$!"; 
open my $out_file4, '>', 'myoutputfilename4.txt' or die "$!"; 

while (<$file>){
  my ($name,$id,@genes) = split /\t/;
  if ($id eq $match) {
     $mio= join("\n",@genes);
     print $mio."\n";

     print $out_file3 $mio."\n"; # print sul file
  }
  if (grep/^$match$/, @genes){
       $mio2=$id;
       print $mio2."\n";

       print $out_file4 $mio2."\n"; # print sul file
   }
}
[download]

I have taken the liberty to move the opening of the files out of the while loop, because it seems inefficient to open the file each time you get a match, but it really depends on you data (how often it matches).

Comment on Re: Unify two files Download Code

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Re^2: Unify two files by pabla23 (Novice) on Nov 10, 2014 at 11:59 UTC
Ok thanks! Now i have this output: APOE APOE FKBP5 CRH with this list i've to enter again in the same file and to find for a single element the different id that are associated; the file have this format: DOID:00001 APOE IL4 RTG5 DOID:00002 FG6 CRH APOE DOID:00003 RTG5 HUTN CRH my output would be: APOE DOID:00001 DOID:00002 CRH DOID:00002 DOID:00003 thanks for your help!!!! Paola	[reply]
Re^3: Unify two files by poj (Abbot) on Nov 10, 2014 at 13:13 UTC
I'm guessing you are looking for the genes for a certain id, and then a looking for all the id's that have those genes. If so try this #!perl use strict; use warnings; my $match = 'DOID:2055'; my $filename = 'do_human_mapping.gmt'; open (my $fh, '<', $filename) or die "open: $!"; my @genes=(); my %gene2id=(); while (<$fh>){ my ($name,$id,@temp) = split /\s+/; if ($id eq $match) { @genes = @temp; } else { for my $gene (@temp){ push @{$gene2id{$gene}},$id } } } for my $gene (@genes){ if (exists $gene2id{$gene}){ print join ' ',$gene,@{$gene2id{$gene}},"\n"; } } __DATA__ DOID:00001 APOE IL4 RTG5 DOID:00002 FG6 CRH APOE DOID:00003 RTG5 HUTN CRH DOID:2055 APOE FKBP5 CRH [download] poj	[reply] [d/l]
Re^4: Unify two files by pabla23 (Novice) on Nov 10, 2014 at 14:01 UTC
Is perfect!!!! Thanks a lot!!! Paola	[reply]