Hello all, Basically I have a list of gene_ids that I do not like (%empty_geneids). And I want to remove all lines in a second file ($ptt_file) that contain these gene_ids. I have tried many variations of this code, all in perl, then 'regressing' to trying to use sed. I know this last attempt using sed is VERY wrong. but I think it explains what I would like to do. I am relatively new so could use some suggestions. thank you 

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`;
}

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In reply to compare lists and delete unwanted from file by AWallBuilder

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