SYNOPSIS
use Bio::DB::GenBank;
$gb = Bio::DB::GenBank->new();
$seq = $gb->get_Seq_by_id('J00522'); # Unique ID, *not always the LOCUS 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.
Running
Alternate methods are described at <http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html>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.''
FEEDBACK
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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.
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:
https://github.com/bioperl/bioperl-live/issues
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
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
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
Routines Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI
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
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
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
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
Routines implemented by Bio::DB::NCBIHelper
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.
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
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()
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()
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.
get_request
Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)
default_format
Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none