# $Id: GenBank.pm 16139 2009-09-18 21:11:23Z cjfields $ # # BioPerl module for Bio::DB::GenBank # # Please direct questions and support issues to # # Cared for by Aaron Mackey # # 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 = Bio::DB::GenBank->new(); $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 = Bio::DB::GenBank->new(-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 # don't want the entire sequence or more options my $gb = Bio::DB::GenBank->new(-format => 'Fasta', -seq_start => 100, -seq_stop => 200, -strand => 1, -complexity => 4); my $seqi = $gb->get_Stream_by_query($query); =head1 DESCRIPTION Allows the dynamic retrieval of L sequence objects from the GenBank database at NCBI, via an Entrez query. WARNING: Please do B 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-Erequest_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). The former behavior prior to bioperl 1.6 was to retrieve these from EBI, but now these are retrieved directly from NCBI. The older behavior can be regained by setting the 'redirect_refseq' flag to a value evaluating to TRUE. =head2 Running Alternate methods are described at L NOTE: strand should be 1 for plus or 2 for minus. Complexity: gi is often a part of a biological blob, containing other gis complexity regulates the display: 0 - get the whole blob 1 - get the bioseq for gi of interest (default in Entrez) 2 - get the minimal bioseq-set containing the gi of interest 3 - get the minimal nuc-prot containing the gi of interest 4 - get the minimal pub-set containing the gi of interest 'seq_start' and 'seq_stop' will not work when setting complexity to any value other than 1. 'strand' works for any setting other than a complexity of 0 (whole glob); when you try this with a GenBank return format nothing happens, whereas using FASTA works but causes display problems with the other sequences in the glob. As Tao Tao says from NCBI, "Better left it out or set it to 1." =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/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =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 the web: http://bugzilla.open-bio.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::GenBank; use strict; use vars qw(%PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE); use base qw(Bio::DB::NCBIHelper); BEGIN { $DEFAULTMODE = 'single'; $DEFAULTFORMAT = 'gbwithparts'; %PARAMSTRING = ( 'batch' => { 'db' => 'nucleotide', 'usehistory' => 'n', 'tool' => 'bioperl'}, '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'}, 'webenv' => { 'query_key' => 'querykey', 'WebEnv' => 'cookie', '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(). Caveat: this normally works, but in rare cases simply passing the accession can lead to odd results, possibly due to unsynchronized NCBI ID servers. Using get_Seq_by_version() is slightly better, but using the unique identifier (GI) and get_Seq_by_id is the most consistent Throws : "id does not exist" exception =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) Note : Caveat: this normally works, but using the unique identifier (GI) and get_Seq_by_id is the most consistent 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) =cut =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; } 1; __END__