Bio::EnsEMBL::Utils SchemaConversion
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Summary
Bio::EnsEMBL::Utils::SchemaConversion - Utility module for Vega schema conversion script
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::ConversionSupport
Data::Dumper
strict
warnings
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()
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
Methods
choose_conversion_typeDescriptionCode
conv_objDescriptionCode
conv_supportDescriptionCode
conv_usageDescriptionCode
do_conversionDescriptionCode
make_schema_up_to_dateDescriptionCode
newDescriptionCode
species_aliasDescriptionCode
Methods description
choose_conversion_typecode    nextTop
  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
conv_objcodeprevnextTop
  Example     : $conversion->conv_obj; 
Description : Provides access to SeqStoreConverter::BasicConverter methods
Return type : SeqStoreConverter::BasicConverter object
Exceptions : none
Caller : general
conv_supportcodeprevnextTop
  Example     : $conversion->conv_support; 
Description : Provides access to Bio::EnsEMBL::Utils::ConversionSupport methods
Return type : Bio::EnsEMBL::Utils::ConversionSuppor object
Exceptions : none
Caller : general
conv_usagecodeprevnextTop
  Example     : $conversion->conv_usage("message")
Description : prints usage information and exits
Return type : none
Exceptions : none
Caller : $Siteroot/utils/vega_schema_conversion
do_conversioncodeprevnextTop
  Example     : $conversion->do_conversion
Description : does the database conversion
Return type : none
Exceptions : none
Caller : $Siteroot/utils/vega_schema_conversion
make_schema_up_to_datecodeprevnextTop
  Example     : $conversion->make_schema_up_to_date
Description : patches schema to latest version
Return type : none
Exceptions : none
Caller : $conversion
newcodeprevnextTop
  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
species_aliascodeprevnextTop
  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
Methods code
choose_conversion_typedescriptionprevnextTop
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;
}
conv_objdescriptionprevnextTop
sub conv_obj {
    my $self = shift;
    return $self->{'converter_object'};
}
conv_supportdescriptionprevnextTop
sub conv_support {
    my $self = shift;
    return $self->{config};
}
conv_usagedescriptionprevnextTop
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;
}
do_conversiondescriptionprevnextTop
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; }
}
make_schema_up_to_datedescriptionprevnextTop
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);
}
newdescriptionprevnextTop
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;
}
species_aliasdescriptionprevnextTop
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";
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.