Bio::DB
GenBank
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Summary
Bio::DB::GenBank - Database object interface to GenBank
Package variables
No package variables defined.
Inherit
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);
Description
Allows the dynamic retrieval of
Bio::Seq sequence objects 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->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). 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.
Alternate methods are described at
http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.htmlNOTE: 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."
Methods
Methods description
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 |
Title : default_format
Usage : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args : none |
Methods code
BEGIN { $DEFAULTMODE = 'single';
$DEFAULTFORMAT = 'gbwithparts';
%PARAMSTRING = (
'batch' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl'},
'query' => { 'usehistory' => 'y',
'tool' => 'bioperl',
'retmode' => 'text'},
'gi' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
'version' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
'single' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
'webenv' => {
'query_key' => 'querykey',
'WebEnv' => 'cookie',
'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
);} | sub get_params
{ my ($self, $mode) = @_;
return defined $PARAMSTRING{$mode} ?
%{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}};
}
} | sub default_format
{ return $DEFAULTFORMAT;
}
1;
__END__ } | General documentation
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
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
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:
https://redmine.open-bio.org/projects/bioperl/
| AUTHOR - Aaron Mackey, Jason Stajich | Top |
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
Title : new
Usage : $gb = Bio::DB::GenBank->new(@options)
Function: Creates a new genbank handle
Returns : a new Bio::DB::Genbank object
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
| Routines Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI | Top |
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
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
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
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
| Routines implemented by Bio::DB::NCBIHelper | Top |
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.
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
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()
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()
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.
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)