Gene: blahblah
Query: FDVKHGAHJKHBHXYJTJGHCJHZGJHJJFVJKFG



##</code><code>##

    Query= 8
         (545 letters)

Database: /ebi/cgg/one/nrdb-filtered/nrdb.filtered
           905,591 sequences; 283,075,510 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

/:swiss|P75505|YC71_MYCPN Hypothetical lipoprotein MPN271 precu...   136  2e-31
>/:swiss|P75505|YC71_MYCPN Hypothetical lipoprotein MPN271 precursor
           (A65_orf251a).//:pironly|S73889|S73889 probable
           lipoprotein A65_orf251a - Mycoplasma pneumoniae (ATCC
           29342) (SGC3)//:gp|AE000055|1674262 conserved
           hypothetical protein, see: MPN643 [Mycoplasma
           pneumoniae]
           Length = 251

 Score =  136 bits (340), Expect = 2e-31
 Identities = 72/121 (59%), Positives = 88/121 (72%), Gaps = 1/121 (0%)
 Frame = -3

Query: 363 KRSFYQELPLLLWFLLLGTVLSACSKVESTKSVHPVKSFKSDLKSLLKETIKQDIDLSKT 184
           K+ F         FLL GT+LSAC+ +++            DL++L+KET  +DIDLSK
Sbjct: 3   KKKFLSRFSFSSLFLLCGTLLSACTGIQA------------DLRNLIKETTGKDIDLSKA 50    



##</code><code>##


#! /usr/local/bin/perl -w

use strict;

my $start_annotation;
my $end_annotation;
my %alignments = ();
my $filename = 'strept_blastx.output';

parse_blast (\$start_annotation, \$end_annotation, \%alignments, $filename);

print $start_annotation;

sub get_file_data
{
my ($filename) = @_;
my @filedata = ();

unless(open (GET_FILE_DATA, $filename))
{
print STDERR "cant open file \"$filename\"\n\n";
exit;
}   
 @filedata = <GET_FILE_DATA>;
close GET_FILE_DATA;
return @filedata;
}


foreach my $key (keys %alignments)
{
print "$key\nxxxxxxxxx\n", $alignments{key}, "\nxxxxxxxxxx\n";
}

print $end_annotation;

exit;

sub parse_blast
{
my ($start_annotation, $end_annotation, $alignments, $filename) = @_;

my $blast_output_file = '';
my $alignment_section = '';

$blast_output_file = join('', get_file_data ($filename));   

   ($$start_annotation, $alignment_section, $$end_annotation) = ($blast_output_file
=~/(.*^ALIGNMENTS\n)(.*)(^ Database:.*)/ms);

%alignments = parse_blast_alignment ($alignment_section);
}

sub parse_blast_alignment
{
my($alignment_section) = @_;
my (%alignment_hash) =();

while ($alignment_section =~ /^>.*\n(^(?!>).*\n)+/gm)
{
my ($value) = $&;
my ($key) = (split(/\|/, $value)) [1];
$alignment_hash{$key} = $value;
}

return %alignment_hash;
}