LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

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NAME

Bio::EnsEMBL::Utils::SchemaConversion - Utility module for Vega schema conversion script

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

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

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

conv_obj

Example     : $conversion->conv_obj; 
Description : Provides access to SeqStoreConverter::BasicConverter methods
Return type : SeqStoreConverter::BasicConverter object
Exceptions  : none
Caller      : general

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

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

do_conversion

Example     : $conversion->do_conversion
Description : does the database conversion 
Return type : none
Exceptions  : none
Caller      : $Siteroot/utils/vega_schema_conversion

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

conv_usage

Example     : $conversion->conv_usage("message")
Description : prints usage information and exits
Return type : none
Exceptions  : none
Caller      : $Siteroot/utils/vega_schema_conversion