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#!/usr/local/bin/perl
# This example will pull out N base pairs upstream of each predicted
# gene in C. elegans
use lib '..','../blib/arch';
use Ace::Sequence;
use strict vars;
use constant HOST => $ENV{ACEDB_HOST} || 'formaggio.cshl.org';
use constant PORT => $ENV{ACEDB_PORT} || 200005;
$|=1;
my $upstream = shift || die "Usage: upstream.pl <size (bp)>\n";
my $db = Ace->connect(-host=>HOST,-port=>PORT) || die "Connection failure: ",Ace->error;
warn "Fetching all predicted genes, please wait....\n";
#my @genes = $db->fetch('Predicted_Gene' => '*');
my @genes = $db->fetch(Predicted_Gene => '4R79.2');
for my $gene(@genes) {
next unless my $seq = Ace::Sequence->new(-seq=>$gene,
-offset => (-$upstream-1),
-length => ($upstream)
);
print $gene,"\t",$seq->dna,"\n";
}
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