#! /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, $file
+name);

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) = ($blas
+t_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;
}
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