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

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NAME

Bio::EnsEMBL::IdMapping::Archiver - create gene_archive and peptide_archive

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).

METHODS

  create_archive
  dump_gene
  dump_tuple
  dump_nc_row
  mapping_session_id

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

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

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

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