Raw content of Bio::EnsEMBL::Utils::SchemaConversion
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Utils::SchemaConversion - Utility module for Vega schema conversion script
=head1 SYNOPSIS
my $serverroot = '/path/to/ensembl';
my $conversion =
Bio::EnsEMBL::Utils::ConversionSupport->new($serverroot);
# parse common options
$conversion->conv_usage->parse_common_options;
# convert from schema 19 to 20+
$conversion->do_conversion()
=head1 DESCRIPTION
This module is a helper module for database conversion, for
both vega-vega and ensembl-vega schemas. It provides a wrapper
around SeqStoreConverter::BasicConverter and the species specific
methods therein. Also provides access to helper functions in
Bio::EnsEMBL::Utils::ConversionSupport
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::SchemaConversion;
use Bio::EnsEMBL::Utils::ConversionSupport;
use strict;
use warnings;
use Data::Dumper;
=head2 new
Example : $conversion->Bio::EnsEMBL::Utils::SchemaConversion->new($serverroot);
Description : Constructor, including an instance of a Bio::EnsEMBL::Utils::ConversionSupport
object. Parses input file and checks input with user
Return type : Bio::EnsEMBL::Utils::SchemaConversion object
Exceptions : thrown if $Siteroot not passed over
Caller : $Siteroot/utils/vega_schema_conversion
=cut
sub new {
my $class = shift;
my $support = shift;
my $self = {};
bless ($self,$class);
$self->{config} = Bio::EnsEMBL::Utils::ConversionSupport->new($support);
$self->conv_support->parse_common_options;
$self->conv_support->parse_extra_options('do_vega_sc=s',
'do_ens_sc=s',
'source_db=s',
'core_sql=s',
'vega_sql=s',
'patch_sql=s',
'force=s',
'do_features=s');
#check input and show help
$self->conv_usage() if ($self->conv_support->param("help"));
$self->conv_usage("configuration file needed") unless ($self->conv_support->param("conffile"));
$self->conv_usage("password for database access needed") unless ($self->conv_support->param("pass"));
$self->conv_usage("can only do conversion to ensembl OR Vega, not both") if ($self->conv_support->param('do_vega_sc') && $self->conv_support->param('do_ens_sc'));
$self->conv_usage("You need to do vega->veg or ensembl->vega conversion") unless ($self->conv_support->param('do_vega_sc') || $self->conv_support->param('do_ens_sc'));
# ask user to confirm parameters to proceed
$self->conv_support->allowed_params('conffile',
'do_vega_sc',
'do_ens_sc',
'host',
'port',
'user',
'pass',
'source_db',
'dbname',
'force',
'do_features',
'verbose',
'logpath',
'logfile',
'core_sql',
'vega_sql',
'patch_sql');
$self->conv_support->confirm_params;
return $self;
}
=head2 conv_support
Example : $conversion->conv_support;
Description : Provides access to Bio::EnsEMBL::Utils::ConversionSupport methods
Return type : Bio::EnsEMBL::Utils::ConversionSuppor object
Exceptions : none
Caller : general
=cut
sub conv_support {
my $self = shift;
return $self->{config};
}
=head2 conv_obj
Example : $conversion->conv_obj;
Description : Provides access to SeqStoreConverter::BasicConverter methods
Return type : SeqStoreConverter::BasicConverter object
Exceptions : none
Caller : general
=cut
sub conv_obj {
my $self = shift;
return $self->{'converter_object'};
}
=head2 species_alias
Example : $self->species_alias
Description : examines name of source database to determine which conversion module to use
Return type : string
Exceptions : die if wrong species name used
Caller : $self
=cut
sub species_alias {
my $self=shift;
my $name = shift;
return 'CanisFamiliaris' if $name =~ /canis/;
return 'HomoSapiens' if $name =~ /homo/;
return 'MusMusculus' if $name =~ /mus/;
return 'DanioRerio' if $name =~ /danio/;
##hack - should use own modules
return 'HomoSapiens' if $name =~ /sus/;
die "invalid name of source database, please check configuration file";
}
=head2 choose_conversion_type
Example : $conversion->choose_conversion_type
Description : compares conversion type (ensembl or vega) and species type with
available modules and chooses that to use for the conversion. Stores
a converter object within the caller
Return type : none
Exceptions : none
Caller : $Siteroot/utils/vega_schema_conversion
=cut
sub choose_conversion_type {
my $self = shift;
my $converter;
my $species;
$species = $self->species_alias($self->conv_support->param('source_db'));
if ($self->conv_support->param('do_vega_sc')) {
$species = "vega::".$species;
eval "require SeqStoreConverter::$species";
if($@) {
warn("Could not require conversion module SeqStoreConverter::$species\ for vega conversion\n" .
"Using SeqStoreConverter::BasicConverter instead:\n$@");
require SeqStoreConverter::BasicConverter;
$species = "BasicConverter";
}
else {
warn "Using conversion module SeqStoreConverter::$species for vega conversion\n";
}
}
else {
eval "require SeqStoreConverter::$species";
if($@) {
warn("Could not require conversion module SeqStoreConverter::$species for Ensembl conversion\n" .
"Using SeqStoreConverter::BasicConverter instead:\n$@");
require SeqStoreConverter::BasicConverter;
$species = "BasicConverter";
}
else {
warn "Using conversion module SeqStoreConverter::$species for Ensembl conversion\n";
}
$self->conv_support->param('vega_sql',0);
}
$converter = "SeqStoreConverter::$species"->new
( $self->conv_support->param('user'),
$self->conv_support->param('pass'),
$self->conv_support->param('host').':'.$self->conv_support->param('port'),
$self->conv_support->param('source_db'),
$self->conv_support->param('dbname'),
$self->conv_support->param('core_sql'),
$self->conv_support->param('vega_sql'),
$self->conv_support->param('force'),
$self->conv_support->param('verbose'),
'',
);
$self->{'converter_object'} = $converter;
}
=head2 do_conversion
Example : $conversion->do_conversion
Description : does the database conversion
Return type : none
Exceptions : none
Caller : $Siteroot/utils/vega_schema_conversion
=cut
sub do_conversion {
my $self= shift;
$self->conv_obj->debug( "\n\n*** converting " . $self->conv_obj->source . " to " .
$self->conv_obj->target() . " ***");
$self->conv_obj->transfer_meta();
$self->conv_obj->create_coord_systems();
$self->conv_obj->create_seq_regions();
$self->conv_obj->create_assembly();
$self->conv_obj->create_attribs();
$self->conv_obj->set_top_level();
$self->conv_obj->transfer_dna();
$self->conv_obj->back_patch_schema();
$self->conv_obj->transfer_genes();
$self->conv_obj->transfer_prediction_transcripts();
if ($self->conv_support->param('do_features')) {
$self->conv_obj->transfer_features();
}
#use this for both ensembl and vega for now,
#but might need changing when vega gets eg transcript modified dates
$self->conv_obj->transfer_vega_stable_ids();
$self->conv_obj->copy_other_tables();
$self->conv_obj->copy_repeat_consensus();
$self->conv_obj->create_meta_coord();
if ($self->conv_support->param('do_vega_sc')) {
$self->conv_obj->copy_other_vega_tables();
$self->conv_obj->update_clone_info();
$self->conv_obj->remove_supercontigs();
$self->conv_obj->copy_internal_clone_names();
$self->conv_obj->copy_assembly_exception;
}
}
=head2 make_schema_up_to_date
Example : $conversion->make_schema_up_to_date
Description : patches schema to latest version
Return type : none
Exceptions : none
Caller : $conversion
=cut
sub make_schema_up_to_date {
my $self = shift;
$self->conv_obj->debug ("\nPatching schema to latest version\n");
my $user = $self->conv_obj->user;
my $pass = $self->conv_obj->password;
my $port = $self->conv_obj->port;
my $host = $self->conv_obj->host;
my $target = $self->conv_obj->target;
my $patch_schema = $self->conv_support->param('patch_sql');
my $cmd = "/usr/local/mysql/bin/mysql -u $user -p$pass -P $port -h $host $target < $patch_schema";
system ($cmd);
}
=head2 conv_usage
Example : $conversion->conv_usage("message")
Description : prints usage information and exits
Return type : none
Exceptions : none
Caller : $Siteroot/utils/vega_schema_conversion
=cut
sub conv_usage {
my $self = shift;
my $msg = shift;
print STDERR "\nMSG: $msg\n" if($msg);
print STDERR <<EOF;
** Source and target databases must be on the same mysql instance
usage: ./conversion_densities.pl <options>
options: --conf <conf_file> configuration file (uses conf/Conversion.ini by default):
fields:
do_vega_sc (do vega conversion: 0 or 1)
do_ens_sc (do ensembl conversion: 0 or 1)
user (a mysql db user with read/write priveleges)
host (eg ecs3f)
port (eg 3310)
source_db (schema 19 source database)
dbname (schema 20+ target database)
force (overwrite existing target database: 0 or 1)
verbose (print out debug statements: 0 or 1)
logpath (location of log file)
do_features (transfer dna- and protein-align features, for debugging: 0 or 1)
core_sql (location of ensembl schema creation script: ensembl/sql/table.sql)
vega_sql (location of creation script for additional vega tables: ensembl/sql/vega_specific_tables.sql)
patch_sql (location of schema patching script: ensembl/sql/vega_latest_schema.sql)
--log name of log_file
--help display this message
EOF
exit;
}
1;
]]>