[Cogs-guts] ensupdate ensid_org.pl,1.1.1.1,1.2

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

Update of /cvsroot/cogs/ensupdate
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv14926

Modified Files:
	ensid_org.pl 
Log Message:
added mysql connect params, add all g/p/t stable ids , bugs

Index: ensid_org.pl
===================================================================
RCS file: /cvsroot/cogs/ensupdate/ensid_org.pl,v
retrieving revision 1.1.1.1
retrieving revision 1.2
diff -C2 -d -r1.1.1.1 -r1.2
*** ensid_org.pl	2 Dec 2005 17:04:01 -0000	1.1.1.1
--- ensid_org.pl	14 Sep 2007 18:07:32 -0000	1.2
***************
*** 1,32 ****
! #!/usr/bin/perl
  use DBI;
! my $user=$ENV{ENS_USER};
! my $pass=$ENV{ENS_PASS};
  my $host=$ENV{ENS_HOST};
  my $sock=$ENV{ENS_SOCK};
  my $sid='ensembl_databases';
! my $cs = "dbi:mysql:$sid:$host;mysql_socket=$sock";
  my $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
  
  my $qh1=$dbh->prepare("select db_name,organism from ens_dbnames where current='yes' and 
! organism<>'multispecies'")||die;
  $qh1->execute||die;
  my $all=$qh1->fetchall_arrayref;
! my $ih1=$dbh->prepare("insert into stable_org(organism,stable_id) values (?,?)")||die;
  foreach my $row (@$all) {
  my ($name,$org)=@$row;
! my $constr = "dbi:mysql:$name:$host;mysql_socket=$sock";
  my $ensdbh= DBI->connect($constr,$user,$pass) or die "connecting: $DBI::errstr" ;
  my $gstblid=$ensdbh->prepare("select stable_id from gene_stable_id")||die;
  my $tstblid=$ensdbh->prepare("select stable_id from transcript_stable_id")||die;
  $gstblid->execute||die;
  $tstblid->execute||die;
! 	while (my $id=$gstblid->fetchrow_array) {
! 		$ih1->execute($org,$id)||die;
! 	}
  my $trs=$tstblid->fetchall_arrayref;
  foreach my $row(@$trs) {
  	my $id=shift @$row;
! 	 $ih1->execute($org,$id)||die;
  }
  }
--- 1,50 ----
! #!/stf/sys/bin/perl
  use DBI;
! my $user=$ENV{ENS_ADMIN};
! my $pass=$ENV{ENS_ADMINPASS};
  my $host=$ENV{ENS_HOST};
  my $sock=$ENV{ENS_SOCK};
+ my $port=$ENV{ENS_PORT};
+ open (MSQLV,'mysql -V|')||die 'Mysql crashed or no mysql installed';
+ my $msqlv=<MSQLV>;
+ close MSQLV;
+ my ($tr,$mver1)=split(/Distrib/,$msqlv);
+ my ($mver,$tr)=split(/,/,$mver1);
+ my ($majormver,@mver)=split(/\./,$mver);
  my $sid='ensembl_databases';
! my $cs = "dbi:mysql:database=$sid;host=$host;";
! $cs .= "mysql_socket=$sock;" if ($sock);
! $cs .= "port=$port;" if ($port);
  my $dbh= DBI->connect($cs,$user,$pass) or die "connecting: $DBI::errstr" ;
  
  my $qh1=$dbh->prepare("select db_name,organism from ens_dbnames where current='yes' and 
! organism<>'multispecies' and db_name like '%_core_%'")||die;
  $qh1->execute||die;
  my $all=$qh1->fetchall_arrayref;
! my $dh1=$dbh->prepare("delete from stable_org")||die;
! $dh1->execute||die;
! my $ih1=$dbh->prepare("insert into stable_org(organism,stable_id,type) values (?,?,?)")||die;
  foreach my $row (@$all) {
  my ($name,$org)=@$row;
! my $constr = "dbi:mysql:$name:$host;mysql_socket=$sock;port=$port;";
  my $ensdbh= DBI->connect($constr,$user,$pass) or die "connecting: $DBI::errstr" ;
  my $gstblid=$ensdbh->prepare("select stable_id from gene_stable_id")||die;
  my $tstblid=$ensdbh->prepare("select stable_id from transcript_stable_id")||die;
+ my $protstablid=$ensdbh->prepare("select stable_id from translation_stable_id")||die;
  $gstblid->execute||die;
  $tstblid->execute||die;
! $protstablid->execute||die;
! while (my $id=$gstblid->fetchrow_array) {
! 		$ih1->execute($org,$id,'gene')||die;
! }
  my $trs=$tstblid->fetchall_arrayref;
  foreach my $row(@$trs) {
  	my $id=shift @$row;
! 	 $ih1->execute($org,$id,'transcript')||die;
  }
+ my $pep=$protstablid->fetchall_arrayref;
+ foreach my $row(@$pep) {
+ 	my $id=shift @$row;
+ 	 $ih1->execute($org,$id,'protein')||die;
  }
+ }
\ No newline at end of file