Bio::EnsEMBL::Utils::SchemaConversion Class Reference

Public Member Functions
public Bio::EnsEMBL::Utils::SchemaConversion	new ()
public Bio::EnsEMBL::Utils::ConversionSuppor	conv_support ()
public SeqStoreConverter::BasicConverter	conv_obj ()
public String	species_alias ()
public void	choose_conversion_type ()
public void	do_conversion ()
public void	make_schema_up_to_date ()
public void	conv_usage ()

Detailed Description

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

Definition at line 29 of file SchemaConversion.pm.

Member Function Documentation

choose_conversion_type()

public void Bio::EnsEMBL::Utils::SchemaConversion::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

Code:

conv_obj()

public SeqStoreConverter::BasicConverter Bio::EnsEMBL::Utils::SchemaConversion::conv_obj

(

)

  Example     :

$conversion->conv_obj; 

  Description : Provides access to SeqStoreConverter::BasicConverter methods
  Return type : SeqStoreConverter::BasicConverter object
  Exceptions  : none
  Caller      : general

Code:

conv_support()

public Bio::EnsEMBL::Utils::ConversionSuppor Bio::EnsEMBL::Utils::SchemaConversion::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

Code:

conv_usage()

public void Bio::EnsEMBL::Utils::SchemaConversion::conv_usage

(

)

  Example     :

$conversion->conv_usage("message")

  Description : prints usage information and exits
  Return type : none
  Exceptions  : none
  Caller      : $Siteroot/utils/vega_schema_conversion

Code:

do_conversion()

public void Bio::EnsEMBL::Utils::SchemaConversion::do_conversion

(

)

  Example     :

$conversion->do_conversion

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

Code:

make_schema_up_to_date()

public void Bio::EnsEMBL::Utils::SchemaConversion::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

Code:

new()

public Bio::EnsEMBL::Utils::SchemaConversion Bio::EnsEMBL::Utils::SchemaConversion::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

Code:

species_alias()

public String Bio::EnsEMBL::Utils::SchemaConversion::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

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Utils/SchemaConversion.pm