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::Utils::ScriptUtils;

SYNOPSIS

DESCRIPTION

METHODS

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?")) {
                    # run some code
                }

                # 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

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

_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)

commify

  Arg[1]      : Int $num - a number to commify
  Example     : print "An easy to read number: ".$self->commify(100000000);
                # 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

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