comparison variant_effect_predictor/Bio/EnsEMBL/Utils/ScriptUtils.pm @ 0:1f6dce3d34e0

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=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::Utils::ScriptUtils;

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 METHODS

=cut

package Bio::EnsEMBL::Utils::ScriptUtils;

use strict;
use warnings;
no warnings 'uninitialized';

use Exporter;
our @ISA = qw(Exporter);

our @EXPORT_OK = qw(
  user_proceed
  commify
  sort_chromosomes
  parse_bytes
  directory_hash
  path_append
  dynamic_use
  inject
);


=head2 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

=cut

sub user_proceed {
  my ($text, $interactive, $default) = @_;

  unless (defined($default)) {
    die("Need a default answer for non-interactive runs.");
  }

  my $input;

  if ($interactive) {
    print "$text\n" if $text;
    print "[y/N] ";
  
    $input = lc(<>);
    chomp $input;
  } else {
    $input = $default;
  }
  
  if ($input eq 'y') {
    return(1);
  } else {
    print "Skipping.\n" if ($interactive);
    return(0);
  }
}


=head2 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

=cut

sub sort_chromosomes {
    my @chromosomes = @_;
    
    return (sort _by_chr_num @chromosomes);
}


=head2 _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)

=cut

sub _by_chr_num {
    my @awords = split /-/, $a;
    my @bwords = split /-/, $b;

    my $anum = $awords[0];
    my $bnum = $bwords[0];

    if ($anum !~ /^[0-9]*$/) {
        if ($bnum !~ /^[0-9]*$/) {
            return $anum cmp $bnum;
        } else {
            return 1;
        }
    }
    if ($bnum !~ /^[0-9]*$/) {
        return -1;
    }

    if ($anum <=> $bnum) {
        return $anum <=> $bnum;
    } else {
        if ($#awords == 0) {
            return -1;
        } elsif ($#bwords == 0) {
            return 1;
        } else {
            return $awords[1] cmp $bwords[1];
        }
    }
}


=head2 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

=cut

sub commify {
  my $num = shift;

  $num = reverse($num);
  $num =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;

  return scalar reverse $num;
}


sub parse_bytes {
  my $bytes = shift;

  my @suffixes = qw(bytes kb Mb Gb Tb);

  my $length = length($bytes);
  my $order = int(($length-1)/3);

  my $parsed = sprintf('%.1f', $bytes/10**(3*$order));

  return "$parsed ".$suffixes[$order];
}


sub directory_hash {
  my $filename = shift;

  my (@md5) = md5_hex($filename) =~ /\G(..)/g;
  return join('/', @md5[0..2]);
}


sub path_append {
  my $path1 = shift;
  my $path2 = shift;

  # default to current directory
  $path1 = '.' unless (defined($path1));

  my $return_path = "$path1/$path2";

  unless (-d $return_path) {
    system("mkdir -p $return_path") == 0 or
      die("Unable to create directory $return_path: $!\n");
  }
  
  return $return_path;
}


=head2 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

=cut

sub inject {
  my $classname = shift;
  my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ?
                                      ($1,$2) : ('::', $classname);
  no strict 'refs';

  # return if module has already been imported
  return 1 if $parent_namespace->{$module.'::'};
  
  eval "require $classname";
  die("Failed to require $classname: $@") if ($@);

  $classname->import();
  
  return 1;
}


sub dynamic_use {
  return inject(@_);
}

1;