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Bio-EnsEMBL-112.0_54
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/ Bio::EnsEMBL::Utils::CliHelper

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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CONTACT

Please email comments or questions to the public Ensembl
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Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::Utils::CliHelper

VERSION

$Revision$

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 another option
push(@$optsd,"print");

# 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});
  ...
  if(defined $opts->{print}) {
  	...
  }
}

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

METHODS

See subroutines.

new()

Description : Construct a new instance of a CliHelper object
Returntype  : Bio::EnsEMBL::Utils:CliHelper
Status      : Under development

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

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

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 if database name matches collection, 1 otherwise.
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

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 DBAdaptors. 
            : Note this can overload connections on a server
Returntype  : Arrayref of Bio::EnsEMBL::DBSQL::DBAdaptor
Status      : Under development

load_registry_for_opts

Arg [1]    	: Hash of options (e.g. parsed from command line options by process_args()) 
Arg [2]     : Optional prefix to use when parsing e.g. dna or master 
Description	: Loads a Registry from the given options hash. If a C<registry> 
              option is given then the code will call C<load_all>. Otherwise
              we use the database parameters given to call 
              C<load_registry_from_db()>.
Returntype  : Integer of the number of DBAdaptors loaded
Status      : Under development