for vega schema conversion

modules/Bio/EnsEMBL/Utils/SchemaConversion.pm

+package Bio::EnsEMBL::Utils::SchemaConversion;
+
+=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 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/code_licence.html for details
+
+=head1 AUTHOR
+
+Steve Trevanion <st3@sanger.ac.uk>
+
+=head1 CONTACT
+
+Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
+
+=cut
+
+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
+  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);
+	return $self;
+}
+
+=head2 conv_support
+
+  Example     : $conversion->conv_support; 
+  Description : This method 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 species_alias
+
+  Example     : $self->species_alias
+  Description : lookup table for common species names and schema conversion modules
+  Return type : string
+  Exceptions  : die if wrong species name used
+  Caller      : $self
+
+=cut
+
+sub species_alias {
+	my $self=shift;
+	my $name = shift;
+	my %aliases = (
+				   dog       => 'CanisFamiliaris',
+				   human     => 'HomoSapiens',
+				   mouse     => 'MusMusculus',
+				   zebrafish => 'DanioRerio'
+			  );
+	return $aliases{$name} || die "invalid species name, 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 $siteroot = $self->conv_support->serverroot;
+	my $converter;
+	my $species;
+	$species = $self->species_alias($self->conv_support->param('species'));
+	if ($self->conv_support->param('do_vega_schema_conversion')) {
+		$species = "vega::".$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";
+		}
+	}
+	$converter = "SeqStoreConverter::$species"->new
+		( $self->conv_support->param('user'), 
+		  $self->conv_support->param('pass'), 
+		  $self->conv_support->param('host'), 
+		  $self->conv_support->param('source_db'), 
+		  $self->conv_support->param('target_db'), 
+		  $siteroot.$self->conv_support->param('core_sql'), 
+		  $siteroot.$self->conv_support->param('vega_sql'), 
+		  $self->conv_support->param('force'), 
+		  $self->conv_support->param('verbose'),
+		  '',
+		);
+	
+	$self->{'converter_object'} = $converter;
+	warn "2. ",Dumper($self);
+
+}
+
+=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->{converter_object}->debug( "\n\n*** converting " . $self->{converter_object}->source . " to " . 
+					   $self->{converter_object}->target() . " ***");
+	$self->{converter_object}->transfer_meta();
+	$self->{converter_object}->create_coord_systems();
+	$self->{converter_object}->create_seq_regions();
+	$self->{converter_object}->create_assembly();
+	$self->{converter_object}->create_attribs();
+	$self->{converter_object}->set_top_level();
+	
+	$self->{converter_object}->transfer_dna();
+	$self->{converter_object}->transfer_genes();
+	$self->{converter_object}->transfer_prediction_transcripts();
+	
+	if ($self->conv_support->param('do_features')) {
+		$self->{converter_object}->transfer_features();
+	}
+	if ($self->conv_support->param('do_vega_schema_conversion')) {
+		$self->{converter_object}->transfer_vega_stable_ids();
+	} else {
+		$self->{converter_object}->transfer_stable_ids();
+	}
+	
+	$self->{converter_object}->copy_other_tables();
+	$self->{converter_object}->copy_repeat_consensus();
+	$self->{converter_object}->create_meta_coord();
+	if ($self->conv_support->param('do_vega_schema_conversion')) {
+		
+		$self->{converter_object}->update_clone_info();
+		$self->{converter_object}->remove_supercontigs();
+		$self->{converter_object}->copy_internal_clone_names();
+	}
+	print STDERR "*** All finished ***\n";
+}
+
+=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;
+
+usage: ./conversion_densities.pl  <options>
+
+options: -pass <password>       the mysql user's password (required)
+
+         -conf <conf_file>      configuration file (required):
+
+                                   fields:
+                                      do_vega_conversion (0 or 1)
+                                      do_ensembl_conversion (0 or 1)
+                                      user (a mysql db user with read/write priveleges)
+                                      host (plus port eg ecs3d:3307)
+                                      species (common name - choose from dog, mouse, human and zebrafish)
+                                      source_db (schema 19 source database)
+                                      target_db (schema 20+ trget database)
+                                      core_sql (location of ensembl schema creation script eg ensembl/sql/table.sql)
+                                      vega_sql (location of creation script for additinoal vega tables eg ensembl/sql/vega_specific_tables.sql)
+                                      force (overwrite existing target database? 0 or 1)
+                                      verbose (print out debug statements 0 or 1)
+                                      do_features (0 or 1 - transfer dna- and protein-align features, for debugging)
+
+         -help                  display this message
+
+EOF
+  exit;
+
+}
+
+1;
+
+
+