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
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

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