#!/bin/perl -w
use strict;
use CGI qw(:standard);
opendir IRESDIR, "/export/home/sylvia/ires";
 
my @iresdir = readdir IRESDIR;
foreach my $dir (@iresdir) {
	push (my @dirlist, $dir);
}
closedir IRESDIR;

foreach my $subdir (my @dirlist) { 
    unless ( $subdir =~ /\.+/ ) {
	opendir SUBDIR, "/export/home/sylvia/ires/$subdir";
	my @filelist = readdir SUBDIR;
	chdir "/export/home/sylvia/ires/$subdir";
	foreach my $file (@filelist) {
		open IRESFILE,  $file;
		while (<IRESFILE>) {
		  if ( $_ =~ /^>gi\|(\d+).*/ ){
		     push (GILIST, $1);
		  }
		}
		close IRESFILE;
	}
	closedir SUBDIR;
    }
}

#####
use Bio::Seq;
use Bio::DB::GenBank;

# creates a general "Sequence object called gb"
my $gb = new Bio::DB::GenBank();
my %specieslist;

my $q = new CGI;
print $q->header,
	$q->start_html( -title => "IRES Elements in Species", -bgcolor =>"#ffffcc" ),
	$q->h2( "IRES Elements Classified by Species" ),
	$q->hr;

# creates a specific Sequence object called seq1
foreach  my $entry (my @GILIST) {
	my $seq1 = $gb->get_Seq_by_acc("$entry") || die "$entry is not a real accession number.\n";
	my $speciesname = $seq1->species->common_name;
	unless ($speciesname eq $specieslist{$entry}) {
		$specieslist{$entry} = $speciesname;
		print p ("Gi# $entry is a $specieslist{$entry} nucleotide sequence.\n");
	}	
}

print	$q->end_html;