comparison variant_effect_predictor/Bio/Biblio/IO.pm @ 0:2bc9b66ada89 draft default tip

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# $Id: IO.pm,v 1.8 2002/10/22 07:45:11 lapp Exp $
#
# BioPerl module for Bio::Biblio::IO
#
# Cared for by Martin Senger <[e-mail]>
# For copyright and disclaimer see below.

# POD documentation - main docs before the code

=head1 NAME

Bio::Biblio::IO - Handling the bibliographic references

=head1 SYNOPSIS

    use Bio::Biblio::IO;

    # getting citations from a file
    $in = Bio::Biblio::IO->new ('-file' => 'myfile.xml' ,
				'-format' => 'medlinexml');
 --- OR ---

    # getting citations from a string
    $in = Bio::Biblio::IO->new ('-data' => '<MedlineCitation>...</MedlineCitation>' ,
				'-format' => 'medlinexml');
 --- OR ---

    # getting citations from a string if IO::String is installed
    use IO::String;
    $in = Bio::Biblio::IO->new ('-fh' => IO::String->new ($citation),
				'-format' => 'medlinexml');

    $in = Bio::Biblio::IO->new(-fh => $io_handle , '-format' => 'medlinexml');

 --- OR ---

    # getting citations from any IO handler
    $in = Bio::Biblio::IO->new('-fh' => $io_handle ,
			       '-format' => 'medlinexml');


    # now, having $in, we can read all citations
    while ( my $citation = $in->next_bibref() ) {
	&do_something_with_citation ($citation);
    }

 --- OR ---

    # again reading all citation but now a callback defined in your
    # code is used (note that the reading starts already when new()
    # is called)
    $io = new Bio::Biblio::IO ('-format'   => 'medlinexml',
			       '-file'     => $testfile,
			       '-callback' => \&callback);
    sub callback {
        my $citation = shift;
	print $citation->{'_identifier'} . "\n";
    }

Now, to actually get a citation in an XML format,
use I<Bio::Biblio> module which returns an XML string:

    use Bio::Biblio;
    my $xml = new Bio::Biblio->get_by_id ('94033980');
    my $reader = Bio::Biblio::IO->new ('-data' => $xml,
				       '-format' => 'medlinexml');

    while (my $citation = $reader->next_bibref()) {
       ... do something here with $citation
       }

And, finally, the resulting citation can be received in different
output formats:

    $io = new Bio::Biblio::IO ('-format' => 'medlinexml',
			       '-result' => 'raw');
 --- OR ---

    $io = new Bio::Biblio::IO ('-format' => 'medlinexml',
			       '-result' => 'medline2ref');

 --- OR ---

    $io = new Bio::Biblio::IO ('-format' => 'pubmedxml',
			       '-result' => 'pubmed2ref');

=head1 DESCRIPTION

Bio::Biblio::IO is a handler module for accessing bibliographic
citations. The citations can be in different formats - assuming that
there is a corresponding module knowing that format in Bio::Biblio::IO
directory (e.g. Bio::Biblio::IO::medlinexml). The format (and the
module name) is given by the argument I<-format>.

Once an instance of C<Bio::Biblio::IO> class is available, the
citations can be read by calling repeatedly method I<next_bibref>:

    while (my $citation = $reader->next_bibref()) {
       ... do something here with $citation
       }

However, this may imply that all citations were already read into the
memory. If you expect a huge amount of citations to be read, you may
choose a I<callback> option. Your subroutine is specified in the
C<new()> method and is called everytime a new citation is available
(see an example above in SYNOPSIS).

The citations returned by I<next_bibref> or given to your callback
routine can be of different formats depending on the argument
I<-result>. One result type is I<raw> and it is represented by a
simple, not blessed hash table:

    $io = new Bio::Biblio::IO ('-result' => 'raw');

What other result formats are available depends on the module who
reads the citations in the first place. At the moment, the following
ones are available:

    $io = new Bio::Biblio::IO ('-result' => 'medline2ref');

This is a default result format for reading citations by the
I<medlinexml> module. The C<medlinexml> module is again the default
one. Which means that you can almost omit arguments (you still need to
say where the citations come from):

    $io = new Bio::Biblio::IO ('-file' => 'data/medline_data.xml');

Another result format available is for PUBMED citations (which is a
super-set of the MEDLINE citations having few more tags):

    $io = new Bio::Biblio::IO ('-format' => 'pubmedxml',
			       '-result' => 'pubmed2ref',
			       '-data'   => $citation);

Or, because C<pubmed2ref> is a default one for PUBMED citations, you can say just:

    $io = new Bio::Biblio::IO ('-format' => 'pubmedxml',
			       '-data'   => $citation);

Both C<medline2ref> and C<pubmed2ref> results are objects defined in
the directory C<Bio::Biblio>.

=head1 SEE ALSO

=over

=item *

An example script I<examples/biblio.pl>. It has many options and its
own help.  The relevant options to this IO module are I<-f>
(specifying what file to read) and I<-O> (specifying what result
format to achieve).

=item *

OpenBQS home page: http://industry.ebi.ac.uk/openBQS

=item *

Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html

=back

=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.

  [e-mail]                  - 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:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR

Martin Senger ([e-mail])

=head1 COPYRIGHT

Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.

This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

=head1 DISCLAIMER

This software is provided "as is" without warranty of any kind.

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are preceded with a _

=cut


# Let the code begin...

package Bio::Biblio::IO;

use strict;
use vars qw(@ISA);

use Bio::Root::Root;
use Bio::Root::IO;
use Symbol();

@ISA = qw(Bio::Root::Root Bio::Root::IO);

my $entry = 0;

sub new {
    my ($caller, @args) = @_;
    my $class = ref ($caller) || $caller;
    
    # if $caller is an object, or if it is an underlying
    # 'real-work-doing' class (e.g. Bio::Biblio::IO::medlinexml) then
    # we want to call SUPER to create and bless an object
    if( $class =~ /Bio::Biblio::IO::(\S+)/ ) {
	my ($self) = $class->SUPER::new (@args);	
	$self->_initialize (@args);
	return $self;

    # this is called only the first time when somebody calls: 'new
    # Bio::Biblio::IO (...)', and it actually loads a 'real-work-doing'
    # module and call this new() method again (unless the loaded
    # module has its own new() method)
    } else { 
	my %param = @args;
	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
	my $format = $param{'-format'} || 
	    $class->_guess_format( $param{-file} || $ARGV[0] ) ||
		'medlinexml';
	$format = "\L$format";	# normalize capitalization to lower case

	# load module with the real implementation - as defined in $format
	return undef unless (&_load_format_module ($format));

	# this will call this same method new() - but rather its
	# upper (object) branche
	return "Bio::Biblio::IO::$format"->new(@args);
    }
}

sub newFh {
  my $class = shift;
  return unless my $self = $class->new(@_);
  return $self->fh;
}


sub fh {
  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;
}

# _initialize is chained for all Bio::Biblio::IO classes

sub _initialize {
    my ($self, @args) = @_;
    # initialize the IO part
    $self->_initialize_io (@args);
}

=head2 next_bibref

 Usage   : $citation = stream->next_bibref
 Function: Reads the next citation object from the stream and returns it.
 Returns : a Bio::Biblio::Ref citation object, or something else
           (depending on the '-result' argument given in the 'new()'
	    method).
 Args    : none

=cut

sub next_bibref {
   my ($self) = shift;
   $self->throw ("Sorry, you cannot read from a generic Bio::Biblio::IO object.");
}

# -----------------------------------------------------------------------------

=head2 _load_format_module

 Usage   : $class->_load_format_module ($format)
 Returns : 1 on success, undef on failure
 Args    : 'format' should contain the last part of the
           name of a module who does the real implementation

It does (in run-time) a similar thing as

   require Bio::Biblio::IO::$format

It throws an exception if it fails to find and load the module
(for example, because of the compilation errors in the module).

=cut

sub _load_format_module {
  my ($format) = @_;
  my ($module, $load, $m);

  $module = "_<Bio/Biblio/IO/$format.pm";
  $load = "Bio/Biblio/IO/$format.pm";

  return 1 if $main::{$module};
  eval {
    require $load;
  };
  if ( $@ ) {
    Bio::Root::Root->throw (<<END);
$load: $format cannot be found or loaded
Exception $@
For more information about the Biblio system please see the Bio::Biblio::IO docs.
END
  ;
    return;
  }
  return 1;
}

=head2 _guess_format

 Usage   : $class->_guess_format ($filename)
 Returns : string with a guessed format of the input data (e.g. 'medlinexml')
 Args    : a file name whose extension can help to guess its format

It makes an expert guess what kind of data are in the given file
(but be prepare that $filename may be empty).

=cut

sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'medlinexml'   if (/\.(xml|medlinexml)$/i);
   return;
}

sub DESTROY {
    my $self = shift;

    $self->close();
}

sub TIEHANDLE {
    my ($class,$val) = @_;
    return bless {'biblio' => $val}, $class;
}

sub READLINE {
  my $self = shift;
  return $self->{'biblio'}->next_bibref() unless wantarray;
  my (@list, $obj);
  push @list, $obj while $obj = $self->{'biblio'}->next_bibref();
  return @list;
}

1;