Bio::DB::GenBank - Database object interface to GenBank
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);
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.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."
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.
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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 : 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
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 : 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() 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) Throws : "acc.version does not exist" exception
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)
Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.