Raw content of Bio::ClusterIO
<![CDATA[# $Id: ClusterIO.pm,v 1.11.2.1 2003/01/21 01:11:17 jason Exp $
#
# BioPerl module for Bio::ClusterIO.pm
#
# Cared for by Andrew Macgregor <andrew@anatomy.otago.ac.nz>
#
# Copyright Andrew Macgregor, Jo-Ann Stanton, David Green
# Molecular Embryology Group, Anatomy & Structural Biology, University of Otago
# http://anatomy.otago.ac.nz/meg
#
# You may distribute this module under the same terms as perl itself
#
# _history
#
# May 7, 2002 - changed from UniGene.pm to more generic ClusterIO.pm
# by Andrew Macgregor
#
# April 17, 2002 - Initial implementation by Andrew Macgregor
# POD documentation - main docs before the code
=head1 NAME
Bio::ClusterIO - Handler for Cluster Formats
=head1 SYNOPSIS
#NB: This example is unigene specific
use Bio::ClusterIO;
$stream = Bio::ClusterIO->new('-file' => "Hs.data",
'-format' => "unigene");
# note: we quote -format to keep older perl's from complaining.
while ( my $in = $stream->next_cluster() ) {
print $in->unigene_id() . "\n";
while ( my $sequence = $in->next_seq() ) {
print $sequence->accession_number() . "\n";
}
}
# Parsing errors are printed to STDERR.
=head1 DESCRIPTION
The ClusterIO module works with the ClusterIO format module to read
various cluster formats such as NCBI UniGene.
=head1 CONSTRUCTORS
=head2 Bio::ClusterIO-E<gt>new()
$str = Bio::ClusterIO->new(-file => 'filename',
-format=>$format);
The new() class method constructs a new Bio::ClusterIO object. The
returned object can be used to retrieve or print cluster
objects. new() accepts the following parameters:
=over 4
=item -file
A file path to be opened for reading.
=item -format
Specify the format of the file. Supported formats include:
unigene *.data UniGene build files.
dbsnp *.xml dbSNP XML files
If no format is specified and a filename is given, then the module
will attempt to deduce it from the filename. If this is unsuccessful,
the main UniGene build format is assumed.
The format name is case insensitive. 'UNIGENE', 'UniGene' and
'unigene' are all supported, as are dbSNP, dbsnp, and DBSNP
=back
=head1 OBJECT METHODS
See below for more detailed summaries. The main methods are:
=head2 $cluster = $str-E<gt>next_cluster()
Fetch the next cluster from the stream.
=head2 TIEHANDLE(), READLINE(), PRINT()
These I've left in here because they were in the SeqIO
module. Feedback appreciated. There they provide the tie interface.
See L<perltie> for more details.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Andrew Macgregor
Email andrew@anatomy.otago.ac.nz
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
#'
# Let the code begin...
package Bio::ClusterIO;
use strict;
use vars qw(@ISA);
use Bio::Root::Root;
use Bio::Root::IO;
@ISA = qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : Bio::ClusterIO->new(-file => $filename, -format => 'format')
Function: Returns a new cluster stream
Returns : A Bio::ClusterIO::Handler initialised with the appropriate format
Args : -file => $filename
-format => format
=cut
my $entry = 0;
sub new {
my ($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::ClusterIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} ||
$class->_guess_format( $param{-file} || $ARGV[0] );
$format = "\L$format"; # normalize capitalization to lower case
return undef unless( $class->_load_format_module($format) );
return "Bio::ClusterIO::$format"->new(@args);
}
}
# _initialize is chained for all ClusterIO classes
sub _initialize {
my($self, @args) = @_;
# initialize the IO part
$self->_initialize_io(@args);
}
=head2 next_cluster
Title : next_cluster
Usage : $cluster = $stream->next_cluster()
Function: Reads the next cluster object from the stream and returns it.
Returns : a L<Bio::ClusterI> compliant object
Args : none
=cut
sub next_cluster {
my ($self, $seq) = @_;
$self->throw("Sorry, you cannot read from a generic Bio::ClusterIO object.");
}
=head2 cluster_factory
Title : cluster_factory
Usage : $obj->cluster_factory($newval)
Function: Get/set the object factory to use for creating the cluster
objects.
Example :
Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
Args : on set, new value (a L<Bio::Factory::ObjectFactoryI>
compliant object or undef, optional)
=cut
sub cluster_factory{
my $self = shift;
return $self->{'cluster_factory'} = shift if @_;
return $self->{'cluster_factory'};
}
=head2 object_factory
Title : object_factory
Usage : $obj->object_factory($newval)
Function: This is an alias to cluster_factory with a more generic name.
Example :
Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
Args : on set, new value (a L<Bio::Factory::ObjectFactoryI>
compliant object or undef, optional)
=cut
sub object_factory{
return shift->cluster_factory(@_);
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL ClusterIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::ClusterIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: could not load $format - for more details on supported formats please see the ClusterIO docs
Exception $@
END
;
}
return $ok;
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function: guess format based on file suffix
Example :
Returns : guessed format of filename (lower case)
Args :
Notes : formats that _filehandle() will guess include unigene and dbsnp
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'unigene' if /\.(data)$/i;
return 'dbsnp' if /\.(xml)$/i;
}
sub DESTROY {
my $self = shift;
$self->close();
}
# I need some direction on these!! The module works so I haven't fiddled with them!
sub TIEHANDLE {
my ($class,$val) = @_;
return bless {'seqio' => $val}, $class;
}
sub READLINE {
my $self = shift;
return $self->{'seqio'}->next_seq() unless wantarray;
my (@list, $obj);
push @list, $obj while $obj = $self->{'seqio'}->next_seq();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'seqio'}->write_seq(@_);
}
1;
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