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::DBSQL::DataFileAdaptor

SYNOPSIS

        my $dfa = $dba->get_DataFileAdaptor();
        my $file = $dfa->fetch_by_dbID(1);
        my $files = $dfa->fetch_all();
        
        my $logic_name_files = $dfa->fetch_all_by_logic_name('bam_alignments');

DESCRIPTION

Provides a database wrapper to store the locations of files and to pull these records back out. DataFile objects can only provide basic information but they can return an intended external database adaptor which can be used to parse the information. This system assumes nothing about the file just that your parser can access it.

Files are supported over any protocol your parser supports and locations can be made absolute, built on the fly or versioned.

METHODS

global_base_path

  Arg[1]        : String; base path 
  Example       : Bio::EnsEMBL::DBSQL::DataFileAdaptor->global_base_path('/base/path');
  Description   : Stores a global value to be used when building data file paths
  Returntype    : String
  Exceptions    : None

get_base_path

  Arg[1]      : String; (optional) base path 
  Example     : $dfa->get_base_path();
  Description : If given the path it will return that path; if not it consults
                $self->global_base_path() for a value. As a last resort
                it will look at the meta table for an entry keyed by
                B<data_file.base_path>
  Returntype  : String
  Exceptions  : Thrown if nothing is found after consulting all three locations

DataFile_to_extensions

  Arg[1]      : Bio::EnsEMBL::DataFile
  Example     : my $exts = $dfa->DataFile_to_extensions($bam_df);
  Description : Returns all expected extensions for the given DataFile type. The
                first returned is the default extension
  Returntype  : ArrayRef
  Exceptions  : Raised if the given file type is not understood

DataFile_to_adaptor

  Arg[1]        : Bio::EnsEMBL::DataFile
  Arg[2]        : (optional) base path
  Arg[3]        : (optional) file type
  Example       : my $bam = $dfa->DataFile_to_adaptor($bam_df);
  Description   : Returns an adaptor instance which will access the given DataFile.
                  Can explicitly request for an adaptor of a given file type (third
                  argument), useful with composite types, e.g. BAM coverage files
                  can be returned as BAM or BIGWIG
  Returntype    : Scalar actual return depends upon the given file type and the
                  requested type
  Exceptions    : Raised if the given file type is not understood or if the requested
                  file type is incompatible with the actual data file type.

fetch_all_by_logic_name

  Args [1]      : String $logic_name for the linked analysis 
  Example       : my $dfs = $dfa->fetch_all_by_logic_name('bam_alignments');
  Description   : Returns all DataFile entries linked to the given analysis 
                logic name
  Returntype    : ArrayRef contains Bio::EnsEMBL::DataFile instances
  Exceptions    : Thrown if logic name does not exist 

fetch_all_by_Analysis

  Args [1]    : Bio::EnsEMBL::Analysis $analysis to look up by 
  Example     : my $dfs = $dfa->fetch_all_by_Analysis($analysis);
  Description : Returns all DataFile entries linked to the given analysis
  Returntype  : ArrayRef contains Bio::EnsEMBL::DataFile instances
  Exceptions  : None

fetch_all_by_CoordSystem

  Args [1]    : Bio::EnsEMBL::CoordSystem $coord_system to look up by 
  Example     : my $dfs = $dfa->fetch_all_by_CoordSystem($cs);
  Description : Returns all DataFile entries linked to the given coordinate
                system. Does B<not> support I<toplevel>
  Returntype  : ArrayRef contains Bio::EnsEMBL::DataFile instances
  Exceptions  : None