#!/usr/bin/perl
use warnings;
use strict;

my %contig;
open my $CNTG, '<', 'contig_names' or die $!;
while (<$CNTG>) {
    chomp;
    s/_//;  # Remove the underscore, as it doesn't appear in the genbank.
    $contig{$_} = 1;
}

local $/ = '//';  # Read the file one record a time.
open my $GB, '<', 'genbank' or die $!;
while (<$GB>) {
    if (my ($id) = /LOCUS \s+ \S+ _ (contig [0-9]+)/x) {
        print if $contig{$id};
    }
}