Raw content of Bio::DB::GenPept # $Id: GenPept.pm,v 1.26 2002/11/21 17:45:59 lstein Exp $ # # BioPerl module for Bio::DB::GenPept # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # completely reworked by Jason Stajich to use Bio::DB::WebDBSeqI 2000-12-12 =head1 NAME Bio::DB::GenPept - Database object interface to GenPept =head1 SYNOPSIS $gb = new Bio::DB::GenPept; $seq = $gb->get_Seq_by_id('195055'); # Unique ID # or ... $seq = $gb->get_Seq_by_acc('DEECTH'); # Accession Number my $seqio = $gb->get_Stream_by_id(['195055', 'DEECTH']); while( my $seq = $seqio->next_seq ) { print "seq is is ", $seq->display_id, "\n"; } =head1 DESCRIPTION Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept database at NCBI, via an Entrez query. WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Batch Entrez support will likely be supported in a future version of DB::GenPept. Currently the only return format supported by NCBI Entrez for GenPept database is GenPept format, so any format specification passed to GenPept will be ignored still be forced to GenPept format (which is just GenBank format). =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://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: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Aaron Mackey, Jason Stajich Email amackey@virginia.edu Email jason@bioperl.org =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::GenPept; use strict; use vars qw(@ISA $DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING ); use Bio::DB::NCBIHelper; @ISA = qw(Bio::DB::NCBIHelper); BEGIN { $DEFAULTMODE = 'single'; $DEFAULTFORMAT = 'gp'; %PARAMSTRING = ( 'batch' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'gi' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'version' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'single' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, ); } # the new way to make modules a little more lightweight sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->request_format($self->default_format); return $self; } =head2 get_params Title : get_params Usage : my %params = $self->get_params($mode) Function: Returns key,value pairs to be passed to NCBI database for either 'batch' or 'single' sequence retrieval method Returns : a key,value pair hash Args : 'single' or 'batch' mode for retrieval =cut sub get_params { my ($self, $mode) = @_; return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}}; } =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 { return $DEFAULTFORMAT; } # from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI =head1 Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('AAC73346'); Function: Gets a Seq objects by accession number Returns : Bio::Seq object Args : accession number to retrive by =head1 Routines implemented by Bio::DB::NCBIHelper =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries =head2 get_Stream_by_acc (2) Title : get_Stream_by_acc Usage : $seq = $db->get_Stream_by_acc($acc); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =head2 request_format Title : request_format Usage : my $format = $self->request_format; $self->request_format($format); Function: Get/Set sequence format retrieval Returns : string representing format Args : $format = sequence format =cut # oberride to force format to be GenPept regardless sub request_format { my ($self) = @_; return $self->SUPER::request_format($self->default_format()); } 1; __END__