Bio::EnsEMBL::Utils::ScriptUtils Class Reference

Public Member Functions
public Boolean	user_proceed ()
public List	sort_chromosomes ()
protected Values	_by_chr_num ()
public A	commify ()
public	parse_bytes ()
public	directory_hash ()
public	path_append ()
public Boolean	inject ()
public	dynamic_use ()

Detailed Description

Synopsis

Description

Definition at line 11 of file ScriptUtils.pm.

Member Function Documentation

_by_chr_num()

protected Values Bio::EnsEMBL::Utils::ScriptUtils::_by_chr_num

(

)

  Example     :

my @sorted = sort _by_chr_num qw(X, 6-COX, 14, 7);

  Description : Subroutine to use in sort for sorting chromosomes. Sorts
                numerically, then alphabetically
  Return type : values to be used by sort
  Exceptions  : none
  Caller      : internal ($self->sort_chromosomes)

Code:

commify()

public A Bio::EnsEMBL::Utils::ScriptUtils::commify

(

)

  Arg[1]      : Int $num - a number to commify
  Example     :

 print "An easy to read number: ".$self->commify(100000000);
@section autotoc_md38 will print 100,000,000

  Description : put commas into a number to make it easier to read
  Return type : a string representing the commified number
  Exceptions  : none
  Caller      : general
  Status      : stable

Code:

directory_hash()

public Bio::EnsEMBL::Utils::ScriptUtils::directory_hash

(

)

Undocumented method

Code:

dynamic_use()

public Bio::EnsEMBL::Utils::ScriptUtils::dynamic_use

(

)

Undocumented method

Code:

inject()

public Boolean Bio::EnsEMBL::Utils::ScriptUtils::inject

(

)

  Arg [1]    : String $classname - The name of the class to require/import
  Example    :

$self->inject('Bio::EnsEMBL::DBSQL::DBAdaptor');

  Description: Requires and imports the methods for the classname provided,
               checks the symbol table so that it doesnot re-require modules
               that have already been required.
  Returntype : true on success
  Exceptions : Warns to standard error if module fails to compile
  Caller     : internal

Code:

parse_bytes()

public Bio::EnsEMBL::Utils::ScriptUtils::parse_bytes

(

)

Undocumented method

Code:

path_append()

public Bio::EnsEMBL::Utils::ScriptUtils::path_append

(

)

Undocumented method

Code:

sort_chromosomes()

public List Bio::EnsEMBL::Utils::ScriptUtils::sort_chromosomes

(

)

  Arg[1]      : (optional) Hashref $chr_hashref - Hashref with chr_name as keys
  Example     :

my $chr = { '6-COX' => 1, '1' => 1, 'X' => 1 };
               my @sorted = $support->sort_chromosomes($chr);

  Description : Sorts chromosomes in an intuitive way (numerically, then
                alphabetically). If no chromosome hashref is passed, it's
                retrieve by calling $self->get_chrlength()
  Return type : List - sorted chromosome names
  Exceptions  : thrown if no hashref is provided
  Caller      : general

Code:

user_proceed()

public Boolean Bio::EnsEMBL::Utils::ScriptUtils::user_proceed

(

)

  Arg[1]      : (optional) String $text - notification text to present to user
  Example     :

 # run a code snipped conditionally
                if ($support->user_proceed("Run the next code snipped?")) {
@section autotoc_md36 run some code
                }
 
@section autotoc_md37 exit if requested by user
                exit unless ($support->user_proceed("Want to continue?"));

  Description : If running interactively, the user is asked if he wants to
                perform a script action. If he doesn't, this section is skipped
                and the script proceeds with the code. When running
                non-interactively, the section is run by default.
  Return type : TRUE to proceed, FALSE to skip.
  Exceptions  : none
  Caller      : general

Code:

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

• ensembl/modules/Bio/EnsEMBL/Utils/ScriptUtils.pm