BioPerl

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Bio/DB/GFF/Adaptor/berkeleydb.pm  view on Meta::CPAN

  }
  close $F;
  my $dna_db = Bio::DB::Fasta->new($file) or $self->throw("Can't reindex sequence file: $@");
  $self->dna_db($dna_db);
  $self->_touch_timestamp;
  return $loaded;
}

sub _mtime {
  my $file = shift;
  my @stat = stat($file);
  return $stat[9];
}

sub _index_file {
  my $self = shift;
  return $self->dsn . "/bdb_features.btree";
}

sub _data_file {
  my $self = shift;

Bio/DB/SeqFeature/Store/berkeleydb.pm  view on Meta::CPAN

  my $self = shift;
  my $index_name = shift;
  my $d = $self->setting($index_name);
  $self->setting($index_name=>shift) if @_;
  $d;
}


sub _mtime {
  my $file = shift;
  my @stat = stat($file);
  return $stat[9];
}

# return names of all the indexes
sub _index_files {
  return qw(names types locations attributes is_indexed);
}

# the directory in which we store our indexes
sub directory {

Bio/Root/Utilities.pm  view on Meta::CPAN

 Title    : file_date
 Usage    : $Util->file_date( filename [,date_format])
 Purpose  : Obtains the date of a given file.
          : Provides flexible formatting via date_format().
 Returns  : String = date of the file as: yyyy-mm-dd (e.g., 1997-10-15)
 Argument : filename = string, full path name for file
          : date_format = string, desired format for date (see date_format()).
          :               Default = yyyy-mm-dd
 Thows    : Exception if no file is provided or does not exist.
 Comments : Uses the mtime field as obtained by stat().

=cut

#--------------
sub file_date {
#--------------
    my ($self, $file, $fmt) = @_;

    $self->throw("No such file: $file") if not $file or not -e $file;

    $fmt ||= 'yyyy-mm-dd';

    my @file_data = stat($file);
    return $self->date_format($fmt, $file_data[9]); # mtime field
}


=head2 untaint

 Title   : untaint
 Purpose : To remove nasty shell characters from untrusted data
         : and allow a script to run with the -T switch.
         : Potentially dangerous shell meta characters:  &;`'\"|*?!~<>^()[]{}$\n\r

Bio/Root/Utilities.pm  view on Meta::CPAN

        printf( "%4d %s\n",   $$href{-NUM_BINARY_FILES}, "binary files");
        printf( "%4d %s\n",   $$href{-NUM_DIRS},         "directories");
    }
}


=head2 file_info

 Title   : file_info
 Purpose : Obtains a variety of date for a given file.
         : Provides an interface to Perl's stat().
 Status  : Under development. Not ready. Don't use!

=cut

#--------------
sub file_info {
#--------------
    my ($self, %param) = @_;
    my ($file, $get, $fmt) = $self->_rearrange([qw(FILE GET FMT)], %param);
    $get ||= 'all';