Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases.
# Do not use this module directly. # get a Bio::DB::NCBIHelper object somehow my $seqio = $db->get_Stream_by_acc(['MUSIGHBA1']); foreach my $seq ( $seqio->next_seq ) { # process seq }
Provides a single place to setup some common methods for querying NCBI web databases. This module just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in postprocess_data().
The base NCBI query URL used is: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)
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. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). 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: deprecated API. Use get_Stream_by_id() instead.
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 : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data
Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format
Title : redirect_refseq Usage : $db->redirect_refseq(1) Function: simple getter/setter which redirects RefSeqs to use Bio::DB::RefSeq Returns : Boolean value Args : Boolean value (optional) Throws : 'unparseable output exception' Note : This replaces 'no_redirect' as a more straightforward flag to redirect possible RefSeqs to use Bio::DB::RefSeq (EBI interface) instead of retrievign the NCBI records
Title : complexity Usage : $db->complexity(3) Function: get/set complexity value Returns : value from 0-4 indicating level of complexity Args : value from 0-4 (optional); if unset server assumes 1 Throws : if arg is not an integer or falls outside of noted range above Note : From efetch docs: 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
Title : strand Usage : $db->strand(1) Function: get/set strand value Returns : strand value if set Args : value of 1 (plus) or 2 (minus); if unset server assumes 1 Throws : if arg is not an integer or is not 1 or 2 Note : This differs from BioPerl's use of strand: 1 = plus, -1 = minus 0 = not relevant. We should probably add in some functionality to convert over in the future.
Title : seq_start Usage : $db->seq_start(123) Function: get/set sequence start location Returns : sequence start value if set Args : integer; if unset server assumes 1 Throws : if arg is not an integer
Title : seq_stop Usage : $db->seq_stop(456) Function: get/set sequence stop (end) location Returns : sequence stop (end) value if set Args : integer; if unset server assumes 1 Throws : if arg is not an integer
Overriding WebDBSeqI method to help newbies to retrieve sequences
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 : _check_id Usage : Function: Returns : A Bio::DB::RefSeq reference or throws Args : $id(s), $string
Title : delay_policy Usage : $secs = $self->delay_policy Function: return number of seconds to delay between calls to remote db Returns : number of seconds to delay Args : none NOTE: NCBI requests a delay of 3 seconds between requests. This method implements that policy.
Title : cookie Usage : ($cookie,$querynum) = $db->cookie Function: return the NCBI query cookie Returns : list of (cookie,querynum) Args : none
NOTE: this information is used by Bio::DB::GenBank in conjunction with efetch.
Title : _parse_response Usage : $db->_parse_response($content) Function: parse out response for cookie Returns : empty Args : none Throws : 'unparseable output exception'
Title : no_redirect Usage : $db->no_redirect($content) Function: Used to indicate that Bio::DB::GenBank instance retrieves possible RefSeqs from EBI instead; default behavior is now to retrieve directly from NCBI Returns : None Args : None Throws : Method is deprecated in favor of positive flag method 'redirect_refseq'
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.