Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Utils::CliHelper Class Reference

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Utils::CliHelper;

  my $cli = Bio::EnsEMBL::Utils::CliHelper-\>new();

  # get the basic options for connecting to a database server
  my $optsd = $cli-\>get_dba_opts();

  # add the print option
  push(@$optsd,"print|p");

  # process the command line with the supplied options plus a reference to a help subroutine
  my $opts = $cli-\>process_args($optsd,\&usage);
  
  # use the command line options to get an array of database details
  for my $db_args (@{$cli-\>get_dba_args_for_opts($opts)}) {
    # use the args to create a DBA
    my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(%{$db_args});
    ...
  }
  
  For adding secondary databases, a prefix can be supplied. For instance, to add a second set of
  db params prefixed with dna (-dnahost -dbport etc.) use the prefix argument with get_dba_opts and 
  get_dba_args_for_opts:
  # get the basic options for connecting to a database server
  my $optsd =
   [ @{ $cli_helper-\>get_dba_opts() }, @{ $cli_helper-\>get_dba_opts('gc') } ];
  # process the command line with the supplied options plus a help subroutine
  my $opts = $cli_helper-\>process_args( $optsd, \&usage );
  # get the dna details
  my ($dna_dba_details) =
    @{ $cli_helper-\>get_dba_args_for_opts( $opts, 1, 'dna' ) };
  my $dna_db =
    Bio::EnsEMBL::DBSQL::DBAdaptor-\>new( %{$dna_dba_details} ) );

Description

Utilities for a more consistent approach to parsing and handling EnsEMBL script command lines
 

Definition at line 52 of file CliHelper.pm.

Available Methods

public Arrayref get_dba_args_for_opts ()
public Arrayref get_dba_opts ()
public get_dbas_for_opts ()
public Hashref process_args ()

Method Documentation

public Arrayref Bio::EnsEMBL::Utils::CliHelper::get_dba_args_for_opts ( )
    Arg [1]     : Hash of options (e.g. parsed from command line options by process_args())
    Arg [2]     : If set to 1, the databases are assumed to have a single species only. Default is 0.
    Arg [3]     : Optional prefix to use when parsing e.g. dna
    Description : Uses the parsed command line options to generate an array of DBAdaptor arguments 
                : (e.g. expands dbpattern, finds all species_ids for multispecies databases)
                : These can then be passed directly to Bio::EnsEMBL::DBSQL::DBAdaptor->new()
    Returntype  : Arrayref of DBA argument hash refs 
    Status      : Under development
 
Code:
click to view
    Arg [1]     : Hash of options (e.g. parsed from command line options by process_args())
    Arg [2]     : If set to 1, the databases are assumed to have a single species only. Default is 0.
    Arg [3]     : Optional prefix to use when parsing e.g. dna
    Description : Uses the parsed command line options to generate an array DBAdaptors. 
                : Note this can overload connections on a server
    Returntype  : Arrayref of Bio::EnsEMBL::DBSQL::DBAdaptor
    Status      : Under development
 

/**

public Arrayref Bio::EnsEMBL::Utils::CliHelper::get_dba_opts ( )
  Arg [1]     : Optional prefix for dbnames e.g. dna
  Description : Retrieves the standard options for connecting to one or more Ensembl databases
  Returntype  : Arrayref of option definitions
  Status      : Under development
 
Code:
click to view
public Bio::EnsEMBL::Utils::CliHelper::get_dbas_for_opts ( )

Undocumented method

Code:
click to view
public Hashref Bio::EnsEMBL::Utils::CliHelper::process_args ( )
    Arg [1]     : Arrayref of supported command line options (e.g. from get_dba_opts)
    Arg [2]     : Ref to subroutine to be invoked when -help or -? is supplied
    Description : Retrieves the standard options for connecting to one or more Ensembl databases
    Returntype  : Hashref of parsed options
    Status      : Under development
 
Code:
click to view

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