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

  Please email comments or questions to the public Ensembl
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  Questions may also be sent to the Ensembl help desk at
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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