diff variant_effect_predictor/Bio/DB/GenPept.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/GenPept.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $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 <[e-mail]>
+#
+# 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.
+
+  [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 - Aaron Mackey, Jason Stajich
+
+Email [e-mail]
+Email [e-mail]
+
+=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__
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