diff --git a/misc-scripts/alt_alleles/alt_alleles.pl b/misc-scripts/alt_alleles/alt_alleles.pl index 004b6e9019420ce789bdb42f4cdd6f22c0bda580..e4f23f37c6fb8a6ffbd62c648aa118822f50b486 100644 --- a/misc-scripts/alt_alleles/alt_alleles.pl +++ b/misc-scripts/alt_alleles/alt_alleles.pl @@ -2,6 +2,15 @@ use strict; use Bio::EnsEMBL::DBSQL::DBAdaptor; use Getopt::Long qw(:config pass_through); +# (make sure api version is correct +# Usage: +# perl alt_alleles.pl -cpass XXXX > & human_release_63_alt_alleles +# +# +# long way +# perl alt_alleles.pl -vhost ens-staging1 -vport 3306 -vdbname homo_sapiens_vega_63_37 -cdbname homo_sapiens_core_63_37 -chost ens-staging1 -cpass XXXX > & human_release_63_alt_alleles +# + my ($vhost, $vpass, $vport, $vdbname, $vuser, $chost, $cpass, $cport, $cdbname, $cuser); GetOptions( @@ -18,10 +27,21 @@ GetOptions( # # Connect to the vgea databse to get the alt allele data. # -my $vega_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $vhost||'ensdb-1-11', + +my $api_version = Bio::EnsEMBL::ApiVersion->software_version(); + +if(!defined($vdbname)){ + $vdbname = "homo_sapiens_vega_".$api_version."_37"; +} + +if(!defined($cdbname)){ + $cdbname = "homo_sapiens_core_".$api_version."_37"; +} + +my $vega_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $vhost||'ens-staging1', -user => $vuser||'ensro', - -port => $vport||5317, - -dbname => $vdbname||"vega_homo_sapiens_20100903_v61_GRCh37"); + -port => $vport||3306, + -dbname => $vdbname||"homo_sapiens_vega_63_37"); @@ -95,11 +115,11 @@ push @{$alt_to_stable{9999}}, "INVALID1"; # Connect to the core database to store the data in. # -my $core_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $chost||'ens-research', +my $core_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $chost||'ens-staging1', -user => $cuser||'ensadmin', -pass => $cpass, -species => "test", - -dbname => $cdbname||"ianl_homo_sapiens_core_62_37g"); + -dbname => $cdbname||"homo_sapiens_core_63_37");