Public Member Functions
public	remove_supercontigs ()

public	copy_other_vega_tables ()

public	copy_current_clone_info ()

public	update_clone_info ()

public	copy_internal_clone_names ()

public	copy_assembly_exception ()

public	back_patch_schema ()

Detailed Description

Definition at line 4 of file VBasicConverter.pm.

Member Function Documentation

◆ back_patch_schema()

public SeqStoreConverter::vega::VBasicConverter::back_patch_schema ( )

Undocumented method

Code:

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sub back_patch_schema {
    my $self = shift;
    $self->debug ("Patching gene, transcript, gene_description and external_db tables back to sch-30");
    my $target = $self->target;
    my $dbh = $self->dbh;
    $dbh->do("DROP TABLE $target.gene");
    $dbh->do( qq(CREATE TABLE $target.gene (
                 `gene_id` int(10) unsigned NOT NULL auto_increment,
                 `type` varchar(40) NOT NULL default '',
                 `analysis_id` int(11) default NULL,
                 `seq_region_id` int(10) unsigned NOT NULL default '0',
                 `seq_region_start` int(10) unsigned NOT NULL default '0',
                 `seq_region_end` int(10) unsigned NOT NULL default '0',
                 `seq_region_strand` tinyint(2) NOT NULL default '0',
                 `display_xref_id` int(10) unsigned default NULL,
                  PRIMARY KEY  (`gene_id`),
                  KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
                  KEY `xref_id_index` (`display_xref_id`),
                  KEY `analysis_idx` (`analysis_id`)
                  ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));
    $dbh->do("DROP TABLE $target.transcript");
    $dbh->do( qq(CREATE TABLE $target.transcript (
                 `transcript_id` int(10) unsigned NOT NULL auto_increment,
                 `gene_id` int(10) unsigned NOT NULL default '0',
                 `seq_region_id` int(10) unsigned NOT NULL default '0',
                 `seq_region_start` int(10) unsigned NOT NULL default '0',
                 `seq_region_end` int(10) unsigned NOT NULL default '0',
                 `seq_region_strand` tinyint(2) NOT NULL default '0',
                 `display_xref_id` int(10) unsigned default NULL,
                 PRIMARY KEY  (`transcript_id`),
                 KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
                 KEY `gene_index` (`gene_id`),
                 KEY `xref_id_index` (`display_xref_id`)
                 ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));
    $dbh->do( qq(CREATE TABLE $target.gene_description (
                 `gene_id` int(10) unsigned NOT NULL default '0',
                 `description` text,
                 PRIMARY KEY  (`gene_id`)
                 ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));
    $dbh->do("DROP TABLE $target.external_db");
    $dbh->do( qq(CREATE TABLE $target.external_db (
                 `external_db_id` int(11) NOT NULL default '0',
                 `db_name` varchar(100) NOT NULL default '',
                 `release` varchar(40) NOT NULL default '',
                 `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL default 'KNOWNXREF',
                 PRIMARY KEY  (`external_db_id`)
                 ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));
}

◆ copy_assembly_exception()

public SeqStoreConverter::vega::VBasicConverter::copy_assembly_exception ( )

Undocumented method

Code:

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◆ copy_current_clone_info()

public SeqStoreConverter::vega::VBasicConverter::copy_current_clone_info ( )

Undocumented method

Code:

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◆ copy_internal_clone_names()

public SeqStoreConverter::vega::VBasicConverter::copy_internal_clone_names ( )

Undocumented method

Code:

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◆ copy_other_vega_tables()

public SeqStoreConverter::vega::VBasicConverter::copy_other_vega_tables ( )

Undocumented method

Code:

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◆ remove_supercontigs()

public SeqStoreConverter::vega::VBasicConverter::remove_supercontigs ( )

Undocumented method

Code:

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◆ update_clone_info()

public SeqStoreConverter::vega::VBasicConverter::update_clone_info ( )

Undocumented method

Code:

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

ensembl/misc-scripts/surgery/SeqStoreConverter/vega/VBasicConverter.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ back_patch_schema()

◆ copy_assembly_exception()

◆ copy_current_clone_info()

◆ copy_internal_clone_names()

◆ copy_other_vega_tables()

◆ remove_supercontigs()

◆ update_clone_info()