#!/usr/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"; }