Bio
ClusterIO
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Summary
Bio::ClusterIO - Handler for Cluster Formats
Package variables
Privates (from "my" definitions)
$entry = 0
Included modules
Inherit
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.
Description
The ClusterIO module works with the ClusterIO format module to read
various cluster formats such as NCBI UniGene.
Methods
Methods description
These I've left in here because they were in the SeqIO module. Feedback appreciated. There they provide the tie interface. See perltie for more details. |
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 |
Title : _load_format_module Usage : *INTERNAL ClusterIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : |
Title : cluster_factory Usage : $obj->cluster_factory($newval) Function: Get/set the object factory to use for creating the cluster objects. Example : Returns : a Bio::Factory::ObjectFactoryI compliant object Args : on set, new value (a Bio::Factory::ObjectFactoryI compliant object or undef, optional) |
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 |
Title : next_cluster Usage : $cluster = $stream->next_cluster() Function: Reads the next cluster object from the stream and returns it. Returns : a Bio::ClusterI compliant object Args : none |
Title : object_factory Usage : $obj->object_factory($newval) Function: This is an alias to cluster_factory with a more generic name. Example : Returns : a Bio::Factory::ObjectFactoryI compliant object Args : on set, new value (a Bio::Factory::ObjectFactoryI compliant object or undef, optional) |
Methods code
sub DESTROY
{ my $self = shift;
$self->close();
}
} |
sub PRINT
{ my $self = shift;
$self->{'seqio'}->write_seq(@_);
}
1; } |
sub READLINE
{ my $self = shift;
return $self->{'seqio'}->next_seq() unless wantarray;
my (@list, $obj);
push @list, $obj while $obj = $self->{'seqio'}->next_seq();
return @list; } |
sub TIEHANDLE
{ my ($class,$val) = @_;
return bless {'seqio' => $val}, $class; } |
sub _guess_format
{ my $class = shift;
return unless $_ = shift;
return 'unigene' if /\.(data)$/i;
return 'dbsnp' if /\.(xml)$/i; } |
sub _initialize
{ my($self, @args) = @_;
$self->_initialize_io(@args); } |
sub _load_format_module
{ my ($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; } |
sub cluster_factory
{ my $self = shift;
return $self->{'cluster_factory'} = shift if @_;
return $self->{'cluster_factory'}; } |
sub new
{ my ($caller,@args) = @_;
my $class = ref($caller) || $caller;
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; my $format = $param{'-format'} ||
$class->_guess_format( $param{-file} || $ARGV[0] );
$format = "\L$format";
return undef unless( $class->_load_format_module($format) );
return "Bio::ClusterIO::$format"->new(@args);
}
}
} |
sub next_cluster
{ my ($self, $seq) = @_;
$self->throw("Sorry, you cannot read from a generic Bio::ClusterIO object."); } |
sub object_factory
{ return shift->cluster_factory(@_); } |
General documentation
$str = Bio::ClusterIO->new(-file => 'filename',
-format=>$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:
-file
A file path to be opened for reading.
-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
See below for more detailed summaries. The main methods are:
$cluster = $str->next_cluster() | Top |
Fetch the next cluster from the stream.
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
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/
AUTHOR - Andrew Macgregor | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _