biofetch documentation.

Do not use this object directly, only access it through the
Bio::Biblio module:

  use Bio::Biblio;
  my $biblio = new Bio::Biblio (-access => 'biofetch');
  my $ref = $biblio->get_by_id('20063307'));

  my $ids = ['20063307', '98276153'];
  my $refio = $biblio->get_all($ids);
  while ($ref = $refio->next_bibref) { 
    print $ref->identifier, "\n";
  }

Title : get_by_id Usage : $entry = $db->get__by_id('20063307') Function: Gets a Bio::Biblio::RefI object by its name Returns : a Bio::Biblio::Medline object Args : the id (as a string) of the reference

Title : get_all Usage : $seq = $db->get_all($ref); Function: Retrieves reference objects from the server 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_by_id(). Example : Returns : a stream of Bio::Biblio::Medline objects Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers.

Title : get_seq_stream Usage : my $seqio = $self->get_seq_sream(%qualifiers) Function: builds a url and queries a web db Returns : a Bio::SeqIO stream capable of producing sequence Args : %qualifiers = a hash qualifiers that the implementing class will process to make a url suitable for web querying

Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data

BEGIN {

    # set the version for version checking
    $VERSION = do { my @r = (q$$Revision: 1.1.2.2 $ =~ /\d+/g); sprintf "%d.%-02d", @r };
    $Revision = q$$Id: biofetch.pm,v 1.1.2.2 2002/03/14 13:21:58 heikki Exp $;

    # you can add your own here theoretically.
    %HOSTS = (
	       'dbfetch' => {
		   baseurl => 'http://%s/cgi-bin/dbfetch?db=medline&style=raw',
		   hosts   => {
		       'ebi'  => 'www.ebi.ac.uk'
		       }
	       }
	      );
    %FORMATMAP = ( 'default' => 'medlinexml'
		   );
    $DEFAULTFORMAT = 'default';

    $DEFAULT_SERVICE = 'http://www.ebi.ac.uk/cgi-bin/dbfetch';

}

my ($class, @args ) = @_; my $self = $class->SUPER::new(@args); $self->{ '_hosts' } = {}; $self->{ '_formatmap' } = {}; $self->hosts(\%HOSTS); $self->formatmap(\%FORMATMAP); $self->{'_default_format'} = $DEFAULTFORMAT; return $self;

sub get_seq_stream {

    my ($self, %qualifiers) = @_;
    my ($rformat, $ioformat) = $self->request_format();
    my $seen = 0;
    foreach my $key ( keys %qualifiers ) {
	if( $key =~ /format/i ) {
	    $rformat = $qualifiers{$key};
	    $seen = 1;
	}
    }
    $qualifiers{'-format'} = $rformat if( !$seen);
    ($rformat, $ioformat) = $self->request_format($rformat);
    
    my $request = $self->get_request(%qualifiers);
    my ($stream,$resp);
    if( $self->retrieval_type =~ /temp/i ) {
	my $dir = $self->io()->tempdir( CLEANUP => 1);
	my ( $fh, $tmpfile) = $self->io()->tempfile( DIR => $dir );
	close $fh;
	my ($resp) = $self->_request($request, $tmpfile);		
	if( ! -e $tmpfile || -z $tmpfile || ! $resp->is_success() ) {
            $self->throw("WebDBSeqI Error - check query sequences!\n");
	}
	$self->postprocess_data('type' => 'file',
				'location' => $tmpfile);	
	# this may get reset when requesting batch mode
	($rformat,$ioformat) = $self->request_format();
	if( $self->verbose > 0 ) {
	    open(ERR, "<$tmpfile");
	    while(<ERR>) { $self->debug($_);}
	} 
	$stream = new Bio::Biblio::IO('-format' => $ioformat,
				      '-file'   => $tmpfile);
    } elsif( $self->retrieval_type =~ /io_string/i ) {
	my ($resp) = $self->_request($request);
        my $content = $resp->content_ref;
	$self->debug( "content is $$content\n");
	if( ! $resp->is_success() || length(${$resp->content_ref()}) == 0 ) {
	    $self->throw("WebDBSeqI Error - check query sequences!\n");	
        }  
	($rformat,$ioformat) = $self->request_format();
	$self->postprocess_data('type'=> 'string',
				'location' => $content);
        print STDERR "str is $$content\n" if ( $self->verbose > 0);
	$stream = new Bio::Biblio::IO('-format' => $ioformat,
#				      '-data'   => "<tag>". $$content. "</tag>");
				      '-data'   => $$content
				      );
    } else { 
	$self->throw("retrieval type " . $self->retrieval_type . 
		     " unsupported\n");
    }
    return $stream;

}

sub postprocess_data {

        my ($self, %args) = @_;
    my $data;
    my $type = uc $args{'type'};
    my $location = $args{'location'};
    if( !defined $type || $type eq '' || !defined $location) {
	return;
    } elsif( $type eq 'STRING' ) {
	$data = $$location; 
    } elsif ( $type eq 'FILE' ) {
	open(TMP, $location) or $self->throw("could not open file $location");
	my @in = <TMP>;
	close TMP;
	$data = join("", @in);
    }

    $data = "<tag>". $data. "</tag>";
    
    if( $type eq 'FILE'  ) {
	open(TMP, ">$location") or $self->throw("could overwrite file $location");
	print TMP $data;
	close TMP;
    } elsif ( $type eq 'STRING' ) {
	${$args{'location'}} = $data;
    }
    
    $self->debug("format is ". $self->request_format(). " data is $data\n");

}

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 list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

BEGIN		Code
new	No description	Code
get_by_id	Description	Code
get_all	Description	Code
get_seq_stream	Description	Code
postprocess_data	Description	Code