Bio::EnsEMBL::IdMapping::Archiver Class Reference

Inheritance diagram for Bio::EnsEMBL::IdMapping::Archiver:

Public Member Functions
public void	create_archive ()
public void	dump_gene ()
public void	dump_tuple ()
public Int	mapping_session_id ()
Public Member Functions inherited from Bio::EnsEMBL::IdMapping::BaseObject
public $this	new ()
public Filehandle	get_filehandle ()
public Boolean	file_exists ()
public SQLStatement	fetch_value_from_db ()
public Int	dump_table_to_file ()
public Int	upload_file_into_table ()
public Bio::EnsEMBL::Utils::Logger	logger ()
public Bio::EnsEMBL::Utils::ConfParser	conf ()
public Bio::EnsEMBL::IdMapping::Cache	cache ()

Detailed Description

Synopsis

my $archiver = Bio::EnsEMBL::IdMapping::Archiver->new(
  -LOGGER => $logger,
  -CONF   => $conf,
  -CACHE  => $cache
);
 
# create gene and peptide archive
$archiver->create_archive($mapping_session_id);
 
# dump existing archive tables to file
my $num_entries =
  $archiver->dump_table_to_file( 'source', 'gene_archive',
  'gene_archive_existing.txt', 1 );

Description

This module creates the gene_archive and peptide_archive
tables. Data is written to a file as tab-delimited text for
loading into a MySQL database (this can be done manually, or using
StableIdmapper->upload_file_into_table()).

An archive entry for a given source gene is created if no target
gene exists, or if any of its transcripts or their translations
changed. Non-coding transcripts only have an entry in gene_archive (i.e.
without a corresponding peptide_archive entry).

Definition at line 39 of file Archiver.pm.

Member Function Documentation

create_archive()

public void Bio::EnsEMBL::IdMapping::Archiver::create_archive

(

)

  Arg[1]      : Int $mapping_session_id - the mapping_session_id for this run
  Example     :

$archiver->create_archive($stable_id_mapper->mapping_session_id);

  Description : Creates the gene_archive and peptide_archive tables and writes
                the data to a tab-delimited file. The decision as to what to
                archive is deferred to dump_gene(), see documentation there for
                details.
  Return type : none
  Exceptions  : Thrown on missing argument.
  Caller      : id_mapping.pl
  Status      : At Risk
              : under development

Code:

dump_gene()

public void Bio::EnsEMBL::IdMapping::Archiver::dump_gene

(

)

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyGene $s_gene - source gene
  Arg[2]      : Bio::EnsEMBL::IdMapping::TinyGene $t_gene - target gene
  Arg[3]      : Filehandle $ga_fh - filehandle for writing gene_archive data
  Arg[4]      : Filehandle $pa_fh - filehandle for writing peptide_archive data
  Example     :

my $target_gene = $gene_mappings{$source_gene->stable_id};
               $archiver->dump_gene($source_gene, $target_gene, $ga_fh, $pa_fh);

  Description : Given a source gene, it will write a gene_achive and
                peptide_achive entry for it if no target gene exists, or if any
                of its transcripts or their translation changed. 
  Return type : none
  Exceptions  : none
  Caller      : create_archive()
  Status      : At Risk
              : under development

Code:

dump_tuple()

public void Bio::EnsEMBL::IdMapping::Archiver::dump_tuple

(

)

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyGene $gene - gene to archive
  Arg[2]      : Bio::EnsEMBL::IdMapping::TinyTrancript $tr - its transcript
  Arg[3]      : Bio::EnsEMBL::IdMapping::TinyTranslation $tl - its translation
  Arg[4]      : Filehandle $ga_fh - filehandle for writing gene_archive data
  Arg[5]      : Filehandle $pa_fh - filehandle for writing peptide_archive data
  Example     :

$archive->dump_tuple($s_gene, $s_tr, $s_tl, $ga_fh, $pa_fh);

  Description : Writes entry lines for gene_archive and peptide_archive.
  Return type : none
  Exceptions  : none
  Caller      : dump_gene()
  Status      : At Risk
              : under development

Code:

mapping_session_id()

public Int Bio::EnsEMBL::IdMapping::Archiver::mapping_session_id

(

)

  Arg[1]      : (optional) Int - mapping_session_id to set
  Example     :

my $msi = $archiver->mapping_session_id;

  Description : Getter/setter for mapping_session_id.
  Return type : Int
  Exceptions  : none
  Caller      : create_archive()
  Status      : At Risk
              : under development

Code:

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

• ensembl/modules/Bio/EnsEMBL/IdMapping/Archiver.pm