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Bio::DB::WebDBSeqI(3) User Contributed Perl DocumentationBio::DB::WebDBSeqI(3)

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/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       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

AUTHOR - Jason Stajich
       Email < jason@bioperl.org >

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	= $db->get_Stream_by_acc([$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_stream(%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.

   mod_perl_api
	Title	: mod_perl_api
	Usage	: $version = self->mod_perl_api
	Function: Returns API version of mod_perl being	used based on set env. variables
	Returns	: mod_perl API version;	if mod_perl isn't loaded, returns 0
	Args	: none

perl v5.24.1			  2017-07-08		 Bio::DB::WebDBSeqI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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