Bio::DB::WebDBSeqI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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.
   http://bugzilla.open-bio.org/
 
 

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