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filter_large_file.pl
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filter_large_file.pl
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#!/usr/bin/perl
#######################################################################################
### ###
### Copyright (C) 2017 Pawel Krawczyk (p.krawczyk@ibb.waw.pl) ###
### ###
### This program is free software: you can redistribute it and/or modify ###
### it under the terms of the GNU General Public License as published by ###
### the Free Software Foundation, either version 3 of the License, or ###
### (at your option) any later version. ###
### ###
### This program is distributed in the hope that it will be useful, ###
### but WITHOUT ANY WARRANTY; without even the implied warranty of ###
### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ###
### GNU General Public License for more details. ###
### ###
### You should have received a copy of the GNU General Public License ###
### along with this program. If not, see <http://www.gnu.org/licenses/>. ###
### ###
#######################################################################################
use strict;
use warnings;
my $ids_file = $ARGV[0];
my $big_file = $ARGV[1];
my $output = $ARGV[2];
my %my_hash = ();
my $i = 0;
open( IDS, "<$ids_file" );
while ( my $line = <IDS> ) {
my ($id) = ( $line =~ /^(\S+)/ );
$my_hash{$id} = 1;
}
close(IDS);
foreach my $a ( sort keys %my_hash ) {
print "$a\n";
}
my $accession;
open( BIG, "<$big_file" );
open( OUT, ">$output" );
while ( my $line = <BIG> ) {
$i++;
if ( $i % 100000 == 0 ) {
print "$i sequences processed\n";
}
($accession) = ( $line =~ /.+\t.+\t(\S+)\...?\t.+\t.+\t.+\t.+$/ );
if ( $my_hash{$accession} ) {
print OUT $line;
print "$accession found!!\n";
}
}
close(OUT);
close(BIG);