Print entire line

[pabla23]

Good Morning All, i've this kind of file:

Charcot-Marie-Tooth disease DOID:10595 KIF20A MTMR2 MTM1 LMNA HOXD10 PRX NEFL EGR2 LITAF GARS NDRG1 ERBB3 HSPB1 EMP2 MPZ ERBB2 PMP22 MFN2 GJB1

Post-traumatic stress disorder DOID:2055 APOE FKBP5 CRH IL2 SLC6A3 MAOB DBH IL8 <(p>

I want to do this:

- as input i've DOID:2055

- into the file i must search this ID

- after i must print all associated "genes" (APOE, FKBP5,...)

At first i split the file in this way:

use strict;
use warnings;
open (FILE, "/Users/Pabli/Desktop/do_human_mapping.gmt");
       
my @array_with_all_fields=();
my @mio=();
       
while(<FILE>){
                   
   @array_with_all_fields=split(/\t/);
   
   if ($array_with_all_fields [1] eq "DOID:2055"){
   print "".$array_with_all_fields[]."\n"; 
   
   }
  }
close FILE;

I don't know the way to print all associated genes that are on the same line....this code infact isn't complete! Can someone help me? Thanks a lot

[Loops]

Hi,

Do you actually have data that has the fields separated by Tab characters as your code suggests? If so are there tabs between each and every gene? Specifying the input file format exactly will determine the solution.

If the input is actually just space characters but you can count on the id you're searching for to be the only field with a colon in it... this works:

my $match = "DOID:2055";

while (<DATA>){
   my ($name,$id,$genes) = m/(.*?)\s+(\S+?:\S+?)\s+(.*)/;
   print "$genes\n" if $id eq $match;
}

__DATA__
Charcot-Marie-Tooth disease DOID:10595 KIF20A MTMR2 MTM1 LMNA HOXD10 P
+RX NEFL EGR2 LITAF GARS NDRG1 ERBB3 HSPB1 EMP2 MPZ ERBB2 PMP22 MFN2 G
+JB1
Post-traumatic stress disorder DOID:2055 APOE FKBP5 CRH IL2 SLC6A3 MAO
+B DBH IL8

[pabla23]

Ok, there is a tab between post-trau/DOID/APOE/FKBP5, they are on the same line

post-traumatic stress disorder DOID:2055 APOE FKBP5 CRH IL2 SLC6A3 MAOB DBH IL8

My input is "DOID:2055" and my output should be:

APOE

FKBP5

CRH

IL2

and the other genes. Sorry for my explanation now is clear? Thanks Paola

[Loops]

ok,

my $filename = '/Users/Pabli/Desktop/do_human_mapping.gmt';
my $match = 'DOID:2055';

open(my $file, '<', $filename) or die "open: $!";

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

The answer to your question then, is to use the assignment idiom above, to name the first two fields, and then use an array to slurp up all the genes that follow on the line. Because the name and id never get lumped into the @genes array, you don't have to go through contortions when it comes time to print.

[CountZero]

Loops has give you some good examples of programs.

But you also see that for each type of query you will need a different program and you will each and every time have to go through your whole file again and again and again.

To avoid that, databases have been invented! Once you insert the data into a database, you can query your database to find the answer to all these (and more!) kind of questions easily by using the standard SQL language.