File to remove strains from acefiles based on a blacklist keyset

remove_strains.pl

#!/usr/bin/env perl

# removes strain objects from an ACE file based on a keyset of strains

# usage:
#  remove_strains.pl -remove KEYSET_FILE -acefile STRAIN_ACE_FILE

use IO::File;
use Getopt::Long;

my ($acefile,$blacklist);

GetOptions(
    '-acefile=s' => \$acefile,
    '-remove=s'  => \$blacklist,
    ) or die("wrong parameters passed\n");
    
die("cannot find files\n") unless (-e $acefile && -e $blacklist);

my %blacklist = %{&get_black_list($blacklist)};

$/="\n\n";
my $inf = new IO::File $acefile,'r' or die(@!);
while (<$inf>){
    if (/Strain : \"(\S+)\"/){
       print $_ unless $blacklist{$1}; 
    }
}

sub get_black_list{
    my ($file)=@_;
    my $inf = new IO::File $file,'r' or die(@!);
    my %ids;
    while (<$inf>){
        if (/Strain : \"(\S+)\"/){
           $ids{$1}=1;   
        }
    }
    return \%ids;
}