Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences # get a WebDBSeqI object somehow # assuming it is a nucleotide db my $seq = $db->get_Seq_by_id('ROA1_HUMAN') 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).

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://bugzilla.bioperl.org/ Email < jason@bioperl.org > 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 = $db->get_Stream_by_acc([$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 = $db->get_Stream_by_gi([$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 = $db->get_Stream_by_version([$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

get_Stream_by_query
Title : get_Stream_by_query Usage : $stream = $db->get_Stream_by_query($query); Function: Gets a series of Seq objects by way of a query string or oject Returns : a Bio::SeqIO stream object Args : $query : A string that uses the appropriate query language for the database or a Bio::DB::QueryI object. It is suggested that you create the Bio::DB::Query object first and interrogate it for the entry count before you fetch a potentially large stream.

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 $username : username (if proxy requires authentication) $password : password (if proxy requires authentication)

authentication
Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass

retrieval_type
Title : retrieval_type Usage : $self->retrieval_type($type); my $type = $self->retrieval_type Function: Get/Set a proxy for retrieval_type (pipeline, io_string or tempfile) Returns : string representing retrieval type Args : $value - the value to store This setting affects how the data stream from the remote web server is processed and passed to the Bio::SeqIO layer. Three types of retrieval types are currently allowed: pipeline Perform a fork in an attempt to begin streaming while the data is still downloading from the remote server. Disk, memory and speed efficient, but will not work on Windows or MacOS 9 platforms. io_string Store downloaded database entry(s) in memory. Can be problematic for batch downloads because entire set of entries must fit in memory. Alll entries must be downloaded before processing can begin. tempfile Store downloaded database entry(s) in a temporary file. All entries must be downloaded before processing can begin. The default is pipeline, with automatic fallback to io_string if pipelining is not available.

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

delay
Title : delay Usage : $secs = $self->delay([$secs]) Function: get/set number of seconds to delay between fetches Returns : number of seconds to delay Args : new value NOTE: the default is to use the value specified by delay_policy(). This can be overridden by calling this method, or by passing the -delay argument to new().

delay_policy
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: The default delay policy is 0s. Override in subclasses to implement delays. The timer has only second resolution, so the delay will actually be +/- 1s.

_sleep
Title : _sleep Usage : $self->_sleep Function: sleep for a number of seconds indicated by the delay policy Returns : none Args : none NOTE: This method keeps track of the last time it was called and only imposes a sleep if it was called more recently than the delay_policy() allows.