use strict;
use warnings;


my $list_file="/g/Viruses/prophage_data/emptySeqList_aa.txt";
my %empty_geneids;
my @header_columns;
my $gene_id;

my @ptt_columns;

open (IN,$list_file); ## list of 83 to remove from ptt file

while(<IN>) {
chomp;
my ($header,$descript)=split(/\s+/,$_);
$header=~ s/^>//g;
@header_columns=split(/_/,$header);
$gene_id=$header_columns[0]."_".$header_columns[1];
$empty_geneids{$gene_id}=1;
print "empty gene_id from list file\t$gene_id\n";
}
close (IN);

my $ptt_file="/g/Viruses/prophage_data/prophage_region.ptt1";
my @ptt_lines;
my @non_empty_lines;
my $ptt_file2;

open (IN,$ptt_file);
@ptt_lines=<IN>;
chomp(@ptt_lines);
close (IN);

open (OUT,">$ptt_file.noEmpties");
foreach my $k1 (keys %empty_geneids){
`sed '/$k1/d' $ptt_file > $ptt_file2`;
`mv $ptt_file2 $ptt_file`;
}