#!usr/bin/perl
#
# read genes into array
#
my @ARGV = [];
my $genesFn = "Genes_list.txt";
open my $genesFh, "<", $genesFn or die "could not open genes file handle!\n";
while (<$genesFh>) {
    chomp;
    push @ARGV, $_;
}


#
# write any matches between annotation line and pattern to results file
#
my $annotationsFn = "GCF_000298275.1_OryAfe1.0_genomic.gff";
my $resultsFn = "answer.gff";
open my $annotationsFh, "<", $annotationsFn or die "could not open annotations file handle!\n";
open my $resultsFh, ">", $resultsFn or die "could not open handle to results file!\n";
while (<$annotationsFh>) {
    chomp;
    if ($_ =~ /ACMSD/ || $_ =~ /CRYM/ || $_ =~ /ARID1B/  {
        print $resultsFh " $_\n";
    }

close $resultsFh;
close $annotationsFh;
close $genesFh;