view release on metacpan or  search on metacpan

lib/CracTools/Config.pm  view on Meta::CPAN

41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
                "/etc/".$CracTools::PACKAGE_NAME
               ], # Not mandatory
    "interactive" => 1, # Not mandatory
    );
 
my $default_content = "# Default configuration file __VERSION__\n#\n\n";
 
$cfg->defaultContent($default_content);
 
 
sub PrintVersion() {
  printf( "Script '%s' from %s v. %s (%s v. %s)\n",
          basename($0),
          $CracTools::PACKAGE_NAME, $CracTools::VERSION,
          $CracTools::PACKAGE_NAME, $CracTools::VERSION);
}
 
 
sub LoadConfig(;$) {
    my ($config_file) = @_;
    if (!defined $config_file) {
        $cfg->update();
        $config_file = $cfg->getPath();
    }
    Config::Simple->import_from($config_file, \%config);
    return $config_file;
}
 
 
sub getConfVar(;$) {
  my $var_name = shift;
  my $die = shift;
  if(defined $config{$var_name}) {
    return $config{$var_name};
  } else {
    if(defined $die && $die eq 1) {
      croak("Config variable \"$var_name\" not found.");
    } else {
      return undef;
    }

lib/CracTools/Utils.pm  view on Meta::CPAN

5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
}
# ABSTRACT: A set of useful functions
$CracTools::Utils::VERSION = '1.251';
use strict;
use warnings;
 
use Carp;
use Fcntl qw( SEEK_SET );
 
 
sub reverseComplement($) {
  my $dna = shift;
 
  # reverse the DNA sequence
  my $revcomp = reverse $dna;
 
  # complement the reversed DNA sequence
  $revcomp =~ tr/ACGTacgt/TGCAtgca/;
  return $revcomp;
}
 
 
sub reverse_tab($) {
  my $string = shift;
  my @tab = split(/,/,$string);
  my $newString;
  if(@tab > 0) {
    for (my $i=$#tab ; $i > 0 ; $i--){
      $newString .= $tab[$i];
      $newString .= ",";
    }
    $newString .= $tab[0];
  }
  return $newString;
}
 
 
sub isVersionGreaterOrEqual($$) {
  my ($v1,$v2) = @_;
  my @v1_nums = split(/\./,$v1);
  my @v2_nums = split(/\./,$v2);
  for(my $i = 0; $i < @v1_nums; $i++) {
    if($v1_nums[$i] >= $v2_nums[$i]) {
      return 1;
    }else {
      return 0;
    }
  }
  if(scalar @v2_nums > @v1_nums) {
    return 0;
  } else {
    return 1;
  }
}
 
 
my %conversion_hash = ( '+' => 1, '-' => '-1', '1' => '+', '-1' => '-');
sub convertStrand($) {
  my $strand = shift;
  return defined $strand? $conversion_hash{$strand} : undef;
}
 
sub removeChrPrefix($) {
  my $string = shift;
  $string =~ s/^chr//i;
  return $string;
}
 
sub addChrPrefix($) {
  my $string = shift;
  return "chr".removeChrPrefix($string);
}
 
 
our $Base64_BITNESS = 6;
our @Base64_ENCODING = qw(A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z 0 1 2 3 4 5 6 7 8 9 + /);
 
# Encode error list into base64
sub encodePosListToBase64 {