File Coverage

blib/lib/Bio/KEGGI.pm

Criterion	Covered	Total	%
statement	15	32	46.8
branch	0	4	0.0
condition			n/a
subroutine	5	7	71.4
pod	1	1	100.0
total	21	44	47.7

package Bio::KEGGI;

=head1 NAME

    Bio::KEGGI - Perl module to parse KEGG genome, ko and pathway files.

=head1 VERSION

    Version 0.1.5

=head1 SYNOPSIS

    use Bio::KEGGI;

    my $keggi = Bio::KEGGI->new(
        -file => 'keggfilename',
        -type => 'filetype',
    );

    while (my $kegg = $keggi->next_rec) {
        print $kegg->id, "\n";
    }

    Now supported KEGG file type are "genome", "ko", "pathway" and "gene".

=head1 DESCRIPTION

    Bio::KEGGI is used to parse KEGG files:

=over

=item genome

    ftp://ftp.genome.jp/pub/kegg/genes/genome

=item ko

    ftp://ftp.genome.jp/pub/kegg/genes/ko

=item pathway

    ftp://ftp.genome.jp/pub/kegg/pathway/pathway

=item gene

    Organism gene entries. such as:

    ftp://ftp.genome.jp/pub/kegg/genes/organisms/aac/A.acidocaldarius.ent

=back

    KEGG data details could be retrieved by module L.

=head1 SEE ALSO

    L also provides a KEGG sequence input/output stream.

=head1 AUTHOR

    Haizhou Liu, zeroliu-at-gmail-dot-com

=head1 BUGS

    This module works for Unix text file format only, which lines end with a
    "\n".

    Please use other softwares, such as dos2unix to convert input file if
    necessary.

=head1 METHODS

=head2 new

    Name:   new
    Desc:   A constructor for a KEGGI object.
    Usage:  Bio::KEGGI->new(
                -file => $file,
		        -type => $type, # A fake parameter
            );
    Args:   $file: A KEGG file: genome, ko, pathway
            $type: 'genome', 'ko', 'pathway' or 'gene'
    Return: A Bio::KEGGI object

=cut

use strict;
use warnings;

# use Smart::Comments;

use Switch;
use Text::Trim;

use Bio::KEGG;

our $VERSION = "v0.1.5";

=begin new
    Name:   new
    Desc:   A constructor for a KEGGI object.
    Usage:  Bio::KEGGI->new(
                -file => $file,
		        -type => $type, # A fake parameter
            );
    Args:   $file: A KEGG file: genome, ko, pathway
            $type: 'genome', 'ko', 'pathway' or 'gene'
    Return: A Bio::KEGGI object
=cut

sub new {
    my ($class, %args) = @_;

    my $self = {};

    my $infile = $args{'-file'};
    my $type = $args{'-type'};

    # Open file
    eval {
        open(INF, $infile) or die;
    };
    if ($@) {
        warn "FATAL: Open KEGG file '$infile' failed!\n$!.\n";
        exit 1;
    }

    $self->{'_FH'} = *INF;

    my $type_module = $class . '::' . $type;

    eval "require $type_module";

#    bless($self, $class.'::'.$type);
    bless($self, $type_module);

    return $self;
}

=begin DESTROY
    Name:   DESTROY
    Desc:   Destructor, Private method
    Return: None
=cut

sub DESTROY {
    my $self = shift;

    my $fh = $self->{'_FH'};

    close $fh;
}


1;