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BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ 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/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://redmine.open-bio.org/projects/bioperl/

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_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.

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