Raw content of Bio::Assembly::IO
<![CDATA[# $Id: IO.pm,v 1.1 2002/11/04 11:47:49 heikki Exp $
#
# BioPerl module for Bio::Assembly::IO
#
# based on the Bio::SeqIO module
# by Ewan Birney <birney@sanger.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# Copyright Robson Francisco de Souza
#
# You may distribute this module under the same terms as perl itself
#
# _history
# POD documentation - main docs before the code
=head1 NAME
Bio::Assembly::IO - Handler for Assembly::IO Formats
=head1 SYNOPSIS
use Bio::Assembly::IO;
$in = Bio::Assembly::IO->new(-file=>"<inputfilename",
-format=>'phrap');
$out = Bio::Assembly::IO->new(-file=>">outputfilename",
-format=>'phrap');
while ( my $seq = $in->next_seq() ) {
$out->write_seq($seq);
}
=head1 DESCRIPTION
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set
(e.g. Bio::Assembly::IO::phrap).
=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 the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - 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@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR
Robson Francisco de Souza
E-mail: rfsouza@citri.iq.usp.br
=head1 CONTRIBUTORS
#
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Assembly::IO;
use Bio::Root::Root;
use Bio::Root::IO;
use strict;
use vars qw(@ISA);
@ISA = qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : Bio::Assembly::IO->new(-file =>$filename,-format=>'format')
Function: Returns a new assembly stream
Returns : A Bio::Assembly::IO::Handler initialised
with the appropriate format
Args : -file => $filename
-format => format
=cut
sub new {
my ($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::Assembly::IO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
$class->throw("Need at least a file name to proceed!")
unless (defined $param{'-file'} || defined $ARGV[0]);
my $format = $param{'-format'} ||
$class->_guess_format( $param{-file} || $ARGV[0] );
$format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
return undef unless( $class->_load_format_module($format) );
return "Bio::Assembly::IO::$format"->new(@args);
}
}
# _initialize is chained for all SeqIO classes
sub _initialize {
my($self, @args) = @_;
# initialize the IO part
$self->_initialize_io(@args);
}
=head2 next_assembly
Title : next_assembly
Usage : $cluster = $stream->next_assembly()
Function: Reads the next assembly object from the stream and returns it.
Returns : a Bio::Assembly::ScaffoldI compliant object
Args : none
=cut
sub next_assembly {
my ($self, $seq) = @_;
$self->throw("Sorry, you cannot read from a generic Bio::Assembly::IO object.");
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL Assembly::IO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::Assembly::IO::" . $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 Assembly::IO 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 includes
only phrap, by now.
=cut
sub _guess_format {
my $class = shift;
my $arg = shift;
return unless defined($arg);
return 'ace' if ($arg =~ /\.ace\.\d+$/i);
return 'phrap' if ($arg =~ /\.phrap\.out$/i);
}
sub DESTROY {
my $self = shift;
$self->close();
}
# I need some direction on these!! The module works so I haven't fiddled with them!
# Me neither! (rfsouza)
sub TIEHANDLE {
my ($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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