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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/GenBank.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,309 @@
+# $Id: GenBank.pm,v 1.47.2.2 2003/07/03 12:31:31 heikki Exp $
+#
+# BioPerl module for Bio::DB::GenBank
+#
+# 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
+# 
+# Added LWP support - Jason Stajich 2000-11-6
+# completely reworked by Jason Stajich 2000-12-8
+# to use WebDBSeqI
+
+# Added batch entrez back when determined that new entrez cgi will
+# essentially work (there is a limit to the number of characters in a
+# GET request so I am not sure how we can get around this).  The NCBI
+# Batch Entrez form has changed some and it does not support retrieval
+# of text only data.  Still should investigate POST-ing (tried and
+# failed) a message to the entrez cgi to get around the GET
+# limitations.
+
+=head1 NAME
+
+Bio::DB::GenBank - Database object interface to GenBank
+
+=head1 SYNOPSIS
+
+    use Bio::DB::GenBank;
+    $gb = new Bio::DB::GenBank;
+
+    $seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID
+
+    # or ...
+
+    $seq = $gb->get_Seq_by_acc('J00522'); # Accession Number
+    $seq = $gb->get_Seq_by_version('J00522.1'); # Accession.version
+    $seq = $gb->get_Seq_by_gi('405830'); # GI Number
+
+    # get a stream via a query string
+    my $query = Bio::DB::Query::GenBank->new
+        (-query   =>'Oryza sativa[Organism] AND EST',
+         -reldate => '30',
+	 -db      => 'nucleotide');
+    my $seqio = $gb->get_Stream_by_query($query);
+
+    while( my $seq =  $seqio->next_seq ) {
+      print "seq length is ", $seq->length,"\n";
+    }
+
+    # or ... best when downloading very large files, prevents
+    # keeping all of the file in memory
+
+    # also don't want features, just sequence so let's save bandwith
+    # and request Fasta sequence
+    $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' , 
+			       -format => 'Fasta');
+    my $seqio = $gb->get_Stream_by_acc(['AC013798', 'AC021953'] );
+    while( my $clone =  $seqio->next_seq ) {
+      print "cloneid is ", $clone->display_id, " ", 
+             $clone->accession_number, "\n";
+    }
+    # note that get_Stream_by_version is not implemented
+
+=head1 DESCRIPTION
+
+Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
+GenBank 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.
+
+Note that when querying for GenBank accessions starting with 'NT_' you
+will need to call $gb-E<gt>request_format('fasta') beforehand, because
+in GenBank format (the default) the sequence part will be left out
+(the reason is that NT contigs are rather annotation with references
+to clones).
+
+Some work has been done to automatically detect and retrieve whole NT_
+clones when the data is in that format (NCBI RefSeq clones).  More
+testing and feedback from users is needed to achieve a good fit of
+functionality and ease of use.
+
+=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::GenBank;
+use strict;
+use vars qw(@ISA %PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE);
+use Bio::DB::NCBIHelper;
+
+@ISA = qw(Bio::DB::NCBIHelper);
+BEGIN {    
+    $DEFAULTMODE   = 'single';
+    $DEFAULTFORMAT = 'gp';
+    %PARAMSTRING = ( 
+		     'batch' => { 'db'     => 'nucleotide',
+				  'usehistory' => 'n',
+				  'tool'   => 'bioperl',
+				  'retmode' => 'text'},
+		     'query' => { 'usehistory' => 'y',
+				  'tool'   => 'bioperl',
+				  'retmode' => 'text'},
+		     'gi' => { 'db'     => 'nucleotide',
+			       'usehistory' => 'n',
+			       'tool'   => 'bioperl',
+			       'retmode' => 'text'},
+		     'version' => { 'db'     => 'nucleotide',
+				    'usehistory' => 'n',
+				    'tool'   => 'bioperl',
+				    'retmode' => 'text'},
+		     'single' => { 'db'     => 'nucleotide',
+				   'usehistory' => 'n',
+				   'tool'   => 'bioperl',
+				   'retmode' => 'text'},
+		     );
+}
+
+# new is in NCBIHelper
+
+# helper method to get db specific options
+
+=head2 new
+
+ Title   : new
+ Usage   : $gb = Bio::DB::GenBank->new(@options)
+ Function: Creates a new genbank handle
+ Returns : New genbank handle
+ Args    : -delay   number of seconds to delay between fetches (3s)
+
+NOTE:  There are other options that are used internally.  By NCBI policy, this
+module introduces a 3s delay between fetches.  If you are fetching multiple genbank
+ids, it is a good idea to use get
+
+=cut
+
+=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}};
+}
+
+# from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI
+
+=head1 Routines Bio::DB::WebDBSeqI from 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 = $db->get_Seq_by_acc($acc);
+  Function: Gets a Seq object by accession numbers
+  Returns : a Bio::Seq object
+  Args    : the accession number as a string
+  Note    : For GenBank, this just calls the same code for get_Seq_by_id()
+  Throws  : "id does not exist" exception
+
+=cut
+
+
+sub get_Seq_by_acc {
+   my ($self,$seqid) = @_;
+   $self->SUPER::get_Seq_by_acc("gb|$seqid");
+}
+
+=head2 get_Seq_by_gi
+
+ Title   : get_Seq_by_gi
+ Usage   : $seq = $db->get_Seq_by_gi('405830');
+ Function: Gets a Bio::Seq object by gi number
+ Returns : A Bio::Seq object
+ Args    : gi number (as a string)
+ Throws  : "gi does not exist" exception
+
+=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 sequence version
+ Returns : A Bio::Seq object
+ Args    : accession.version (as a string)
+ Throws  : "acc.version does not exist" exception
+
+=head1 Routines implemented by Bio::DB::NCBIHelper
+
+=head2 get_Stream_by_query
+
+  Title   : get_Stream_by_query
+  Usage   : $seq = $db->get_Stream_by_query($query);
+  Function: Retrieves Seq objects from Entrez '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    : $query :   An Entrez query string or a
+            Bio::DB::Query::GenBank object.  It is suggested that you
+            create a Bio::DB::Query::GenBank object and get the entry
+            count before you fetch a potentially large stream.
+
+=cut
+
+=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
+
+  Title   : get_Stream_by_acc
+  Usage   : $seq = $db->get_Stream_by_acc([$acc1, $acc2]);
+  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()
+
+=cut
+
+=head2 get_Stream_by_gi
+
+  Title   : get_Stream_by_gi
+  Usage   : $seq = $db->get_Seq_by_gi([$gi1, $gi2]);
+  Function: Gets a series of Seq objects by gi numbers
+  Returns : a Bio::SeqIO stream object
+  Args    : $ref : a reference to an array of gi numbers for
+                   the desired sequence entries
+  Note    : For GenBank, this just calls the same code for get_Stream_by_id()
+
+=head2 get_Stream_by_batch
+
+  Title   : get_Stream_by_batch
+  Usage   : $seq = $db->get_Stream_by_batch($ref);
+  Function: Retrieves Seq objects from Entrez 'en masse', rather than one
+            at a time.
+  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: This method is redundant and deprecated.  Use get_Stream_by_id()
+instead.
+
+=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)
+
+1;
+__END__