1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
|
#!/usr/local/bin/perl
# This example will pull out N base pairs upstream of each predicted
# gene in C. elegans
use lib '../blib/lib','../blib/arch';
use Ace::Sequence::Multi;
use strict vars;
use constant HOST => 'stein.cshl.org';
use constant MAPS => 300000;
use constant GENES => 300001;
$|=1;
my $upstream = shift || die "Usage: upstream.pl <size (bp)>\n";
my $db1 = Ace->connect(-host=>HOST,-port=>MAPS) || die "Connection failure: ",Ace->error;
my $db2 = Ace->connect(-host=>HOST,-port=>GENES) || die "Connection failure: ",Ace->error;
warn "Fetching all predicted genes, please wait....\n";
my @genes = $db2->fetch('Predicted_Gene' => '*');
for my $gene(@genes) {
my $seq = Ace::Sequence->new(-seq=>$gene,-offset=>(- $upstream),-length=>$upstream);
next unless my $s = Ace::Sequence->new(-db=>$db1,
-name => $seq->parent,
-offset => $seq->offset,
-length => $seq->length);
print $gene,"\t",$s->dna,"\n";
}
|
