[Cogs-guts] ensupdate generate_keywords.pl,NONE,1.1

[kirovs <ki...@us...>]

Update of /cvsroot/cogs/ensupdate
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv16156

Added Files:
	generate_keywords.pl 
Log Message:
generate mysql table for searching ensembl

--- NEW FILE: generate_keywords.pl ---
#!/stf/sys/bin/perl
use BMS::ensembl::talk;
use strict;
my %uh;
my $host=$ENV{ENS_HOST};
my $port=$ENV{ENS_PORT};
my $drv=$ENV{ENS_DRV};
my $user=$ENV{ENS_ADMIN};
my $pass=$ENV{ENS_ADMINPASS};
my $ens=new BMS::ensembl::talk(DRV=>$drv,HOST=>$host,ADD=>$port,PASS=>$pass,USER=>$user)||die;
my @tables=$ens->marttables('xref');
my $dbh=$ens->get_mart;
foreach my $table (@tables) {
	next if ($table=~/concat/);
	my $sth=$dbh->prepare("select gene_stable_id,transcript_stable_id,translation_stable_id,display_id_list,dbprimary_id from $table")||die;
	$sth->execute||die;
	my $all=$sth->fetchall_arrayref;
	$sth->finish;
	foreach my $row (@$all) {
		my ($gid,$tid,$pid,$list,$ppid)=@$row;
		$list=~s/[,:]/|/g if ($list);
		my $com;
		if ($list) {
			$com=$ppid?"$ppid|$list|":"$list|";
		}
		else { $com="$ppid|"; }
		next if ($com eq '|');
		if ($gid) {
			unless (exists($uh{$gid})) {$uh{$gid}='|'; }
			$uh{$gid} .= $com;
			next;
		}
		if ($tid) {
			unless (exists($uh{$tid})) {$uh{$tid}='|'; }
			$uh{$tid} .= $com;
			next;
		}
		if ($pid) {
			unless (exists($uh{$pid})) {$uh{$pid}='|'; }
			$uh{$pid} .= $com;
			next;
		}
	}
}
$dbh->disconnect;
my $dbh=$ens->{ENSdbh1};
my $sth=$dbh->prepare("update stable_org set keywords=? where stable_id=?")||die;
foreach my $key (keys %uh) {
	$sth->execute($uh{$key},$key);
}
$sth->finish;
$dbh->disconnect;