/ 
bioperl-1.0.2
/ Bio::DB::WebDBSeqI

NAME

Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences

SYNOPSIS

# get a WebDBSeqI object somehow
# assuming it is a nucleotide db
my $seq = $db->get_Seq_by_id('ROA1_HUMAN')

DESCRIPTION

Provides core set of functionality for connecting to a web based database for retriving sequences.

Users wishing to add another Web Based Sequence Dabatase will need to extend this class (see Bio::DB::SwissProt or Bio::DB::NCBIHelper for examples) and implement the get_request method which returns a HTTP::Request for the specified uids (accessions, ids, etc depending on what query types the database accepts).

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.

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/MailList.shtml  - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@chg.mc.duke.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args    : accession number (as a string)
Throws  : "acc 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)
Throws  : "acc.version does not exist" exception

get_request

Title   : get_request
Usage   : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns : 
Args    : %qualifiers = a hash of qualifiers (ids, format, etc)

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 = $db->get_Seq_by_acc([$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_version

Title   : get_Stream_by_version
Usage   : $seq = $db->get_Seq_by_version([$version1, $version2]);
Function: Gets a series of Seq objects by accession.versions
Returns : a Bio::SeqIO stream object
Args    : $ref : a reference to an array of accession.version strings for
                 the desired sequence entries
Note    : For GenBank, this is implemeted in NCBIHelper

default_format

Title   : default_format
Usage   : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args    : none

request_format

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

get_seq_stream

Title   : get_seq_stream
Usage   : my $seqio = $self->get_seq_sream(%qualifiers)
Function: builds a url and queries a web db
Returns : a Bio::SeqIO stream capable of producing sequence
Args    : %qualifiers = a hash qualifiers that the implementing class 
          will process to make a url suitable for web querying

url_base_address

Title   : url_base_address
Usage   : my $address = $self->url_base_address or 
          $self->url_base_address($address)
Function: Get/Set the base URL for the Web Database
Returns : Base URL for the Web Database 
Args    : $address - URL for the WebDatabase

proxy

Title   : proxy
Usage   : $httpproxy = $db->proxy('http')  or 
          $db->proxy(['http','ftp'], 'http://myproxy' )
Function: Get/Set a proxy for use of proxy
Returns : a string indicating the proxy
Args    : $protocol : an array ref of the protocol(s) to set/get
          $proxyurl : url of the proxy to use for the specified protocol

retrieval_type

Title   : retrieval_type
Usage   : $self->retrieval_type($type);
          my $type = $self->retrieval_type
Function: Get/Set a proxy for retrieval_type (io_string or tempfile)
Returns : string representing retrieval type
Args    : $value - the value to store

url_params

Title   : url_params
Usage   : my $params = $self->url_params or 
          $self->url_params($params)
Function: Get/Set the URL parameters for the Web Database
Returns : url parameters for Web Database
Args    : $params - parameters to be appended to the URL for the WebDatabase

ua

Title   : ua
Usage   : my $ua = $self->ua or 
          $self->ua($ua)
Function: Get/Set a LWP::UserAgent for use
Returns : reference to LWP::UserAgent Object
Args    : $ua - must be a LWP::UserAgent

postprocess_data

 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