G'day ag88,

Welcome to the monastery.

You can treat each BLASTP block as a single record. This makes it easy to identify which have "0 hits found", and print their "gi" values. (In the code below, I've truncated the data lines to 60 characters.)

#!/usr/bin/env perl -l

use strict;
use warnings;

{
    local $/ = "# BLASTP 2.2.28+\n";

    while (<DATA>) {
        print /gi\|(\d+)/ if /0 hits found/;
    }
}

__DATA__
# BLASTP 2.2.28+
# Query: gi|338220664|gb|EGP06123.1| hypothetical protein GE
# Database: nr-25sep
# Fields: query id, subject id, % identity, alignment length
# 2 hits found
gi|338220664|gb|EGP06123.1| gi|45383702|ref|NP_989542.1|    
gi|338220664|gb|EGP06123.1| gi|15419940|gb|AAK97214.1|  44.1
# BLASTP 2.2.28+
# Query: gi|338220666|gb|EGP06125.1| hypothetical protein GE
# Database: nr-25sep
# 0 hits found
# BLASTP 2.2.28+
# Query: gi|338220651|gb|EGP06111.1| hypothetical protein GE
# Database: nr-25sep
# 0 hits found
[download]

Output:

338220666
338220651
[download]

See "perlvar: Variables related to filehandles" for a discussion of this usage of "$/" (the input record separator).