Raw content of Bio::DB::DBFetch
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# $Id: DBFetch.pm,v 1.8 2002/12/22 22:02:13 lstein Exp $
#
# BioPerl module for Bio::DB::DBFetch
#
# Cared for by Heikki Lehvaslaiho <Heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::DBFetch - Database object for retrieving using the dbfetch script
=head1 SYNOPSIS
#do not use this module directly
=head1 DESCRIPTION
Allows the dynamic retrieval of entries from databases using the
dbfetch script at EBI:
L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch>.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
This is a superclass which is called by instantiable subclasses with
correct parameters.
=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://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 - Heikki Lehvaslaiho
Email Heikki Lehvaslaiho E<lt>Heikki@ebi.ac.ukE<gt>
=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::DB::DBFetch;
use strict;
use vars qw(@ISA $MODVERSION $DEFAULTFORMAT $DEFAULTLOCATION
$DEFAULTSERVERTYPE);
$MODVERSION = '0.1';
use HTTP::Request::Common;
use Bio::DB::WebDBSeqI;
@ISA = qw(Bio::DB::WebDBSeqI);
# the new way to make modules a little more lightweight
BEGIN {
# global vars
$DEFAULTSERVERTYPE = 'dbfetch';
$DEFAULTLOCATION = 'ebi';
}
=head1 Routines from Bio::DB::WebDBSeqI
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
sub get_request {
my ($self, @qualifiers) = @_;
my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)],
@qualifiers);
$self->throw("Must specify a value for UIDs to fetch")
unless defined $uids;
my $tmp;
my $format_string = '';
$format ||= $self->default_format;
($format, $tmp) = $self->request_format($format);
$format_string = "&format=$format" if $format ne $self->default_format;
my $url = $self->location_url();
my $uid;
if( ref($uids) =~ /ARRAY/i ) {
$uid = join (',', @$uids);
$self->warn ('The server will accept maximum of 50 entries in a request. The rest are ignored.')
if scalar @$uids >50;
} else {
$uid = $uids;
}
return GET $url. $format_string. '&id='. $uid;
}
=head2 postprocess_data
Title : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr);
Function: process downloaded data before loading into a Bio::SeqIO
Returns : void
Args : hash with two keys - 'type' can be 'string' or 'file'
- 'location' either file location or string
reference containing data
=cut
# remove occasional blank lines at top of web output
sub postprocess_data {
my ($self, %args) = @_;
if ($args{type} eq 'string') {
${$args{location}} =~ s/^\s+//; # get rid of leading whitespace
}
elsif ($args{type} eq 'file') {
open F,$args{location} or $self->throw("Cannot open $args{location}: $!");
my @data = <F>;
for (@data) {
last unless /^\s+$/;
shift @data;
}
open F,">$args{location}" or $self->throw("Cannot write to $args{location}: $!");
print F @data;
close F;
}
}
=head2 default_format
Title : default_format
Usage : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args : none
=cut
sub default_format {
my ($self) = @_;
return $self->{'_default_format'};
}
=head1 Bio::DB::DBFetch specific routines
=head2 get_Stream_by_id
Title : get_Stream_by_id
Usage : $seq = $db->get_Stream_by_id($ref);
Function: Retrieves Seq objects from the server 'en masse', rather than one
at a time. For large numbers of sequences, this is far superior
than get_Stream_by_[id/acc]().
Example :
Returns : a Bio::SeqIO stream object
Args : $ref : either an array reference, a filename, or a filehandle
from which to get the list of unique ids/accession numbers.
NOTE: for backward compatibility, this method is also called
get_Stream_by_batch.
=cut
sub get_Stream_by_id {
my ($self, $ids) = @_;
return $self->get_seq_stream('-uids' => $ids, '-mode' => 'batch');
}
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : version number (as a string)
Throws : "version does not exist" exception
=cut
sub get_Seq_by_version {
my ($self,$seqid) = @_;
my $seqio = $self->get_Stream_by_acc([$seqid]);
$self->throw("version does not exist") if( !defined $seqio );
return $seqio->next_seq();
}
=head2 request_format
Title : request_format
Usage : my ($req_format, $ioformat) = $self->request_format;
$self->request_format("genbank");
$self->request_format("fasta");
Function: Get/Set sequence format retrieval. The get-form will normally not
be used outside of this and derived modules.
Returns : Array of two strings, the first representing the format for
retrieval, and the second specifying the corresponding SeqIO format.
Args : $format = sequence format
=cut
sub request_format {
my ($self, $value) = @_;
if( defined $value ) {
$value = lc $value;
$self->{'_format'} = $value;
return ($value, $value);
}
$value = $self->{'_format'};
if( $value and defined $self->formatmap->{$value} ) {
return ($value, $self->formatmap->{$value});
} else {
# Try to fall back to a default.
return ($self->default_format, $self->default_format );
}
}
=head2 servertype
Title : servertype
Usage : my $servertype = $self->servertype
$self->servertype($servertype);
Function: Get/Set server type
Returns : string
Args : server type string [optional]
=cut
sub servertype {
my ($self, $servertype) = @_;
if( defined $servertype && $servertype ne '') {
$self->throw("You gave an invalid server type ($servertype)".
" - available types are ".
keys %{$self->hosts}) unless( $self->hosts->{$servertype} );
$self->{'_servertype'} = $servertype;
}
$self->{'_servertype'} = $DEFAULTSERVERTYPE unless $self->{'_servertype'};
return $self->{'_servertype'};
}
=head2 hostlocation
Title : hostlocation
Usage : my $location = $self->hostlocation()
$self->hostlocation($location)
Function: Set/Get Hostlocation
Returns : string representing hostlocation
Args : string specifying hostlocation [optional]
=cut
sub hostlocation {
my ($self, $location ) = @_;
$location = lc $location;
my $servertype = $self->servertype;
$self->throw("Must have a valid servertype defined not $servertype")
unless defined $servertype;
my %hosts = %{$self->hosts->{$servertype}->{'hosts'}};
if( defined $location && $location ne '' ) {
if( ! $hosts{$location} ) {
$self->throw("Must specify a known host, not $location,".
" possible values (".
join(",", sort keys %hosts ). ")");
}
$self->{'_hostlocation'} = $location;
}
$self->{'_hostlocation'} = $DEFAULTLOCATION unless $self->{'_hostlocation'};
return $self->{'_hostlocation'};
}
=head2 location_url
Title : location
Usage : my $url = $self->location_url()
Function: Get host url
Returns : string representing url
Args : none
=cut
sub location_url {
my ($self) = @_;
my $servertype = $self->servertype();
my $location = $self->hostlocation();
if( ! defined $location || !defined $servertype ) {
$self->throw("must have a valid hostlocation and servertype set before calling location_url");
}
return sprintf($self->hosts->{$servertype}->{'baseurl'},
$self->hosts->{$servertype}->{'hosts'}->{$location});
}
=head1 Bio::DB::DBFetch routines
These methods allow subclasses to pass parameters.
=head2 hosts
Title : hosts
Usage :
Function: get/set for host hash
Returns :
Args : optional hash
=cut
sub hosts {
my ($self, $value) = @_;
if (defined $value) {
$self->{'_hosts'} = $value;
}
unless (exists $self->{'_hosts'}) {
return ('');
} else {
return $self->{'_hosts'};
}
}
=head2 formatmap
Title : formatmap
Usage :
Function: get/set for format hash
Returns :
Args : optional hash
=cut
sub formatmap {
my ($self, $value) = @_;
if (defined $value) {
$self->{'_formatmap'} = $value;
}
unless (exists $self->{'_formatmap'}) {
return ('');
} else {
return $self->{'_formatmap'};
}
}
1;
__END__
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