Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases
Index
Code Index:
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.
Title : default_format
Usage : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args : none
Title : request_format
Usage : my ($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 : $version = self->mod_perl_api
Function: Returns API version of mod_perl being used based on set env. variables
Returns : mod_perl API version; if mod_perl isn't loaded, returns 0
Args : none
#
# BioPerl module for Bio::DB::WebDBSeqI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
# Let the code begin...
package Bio::DB::WebDBSeqI;
use strict;
use vars qw($MODVERSION %RETRIEVAL_TYPES $DEFAULT_RETRIEVAL_TYPE
$DEFAULTFORMAT $LAST_INVOCATION_TIME @ATTRIBUTES);
use Bio::SeqIO;
use Bio::Root::IO;
use LWP::UserAgent;
use POSIX 'setsid';
use HTTP::Request::Common;
use HTTP::Response;
use File::Spec;
use IO::Pipe;
use IO::String;
use Bio::Root::Root;
use base qw(Bio::DB::RandomAccessI);
BEGIN {
$MODVERSION = '0.8';
%RETRIEVAL_TYPES = ('io_string' => 1,
'tempfile' => 1,
'pipeline' => 1,
);
$DEFAULT_RETRIEVAL_TYPE = 'pipeline';
$DEFAULTFORMAT = 'fasta';
$LAST_INVOCATION_TIME = 0;
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($baseaddress, $params, $ret_type, $format,$delay,$db) =
$self->_rearrange([qw(BASEADDRESS PARAMS RETRIEVALTYPE FORMAT DELAY DB)],
@args);
$ret_type = $DEFAULT_RETRIEVAL_TYPE unless ( $ret_type);
$baseaddress && $self->url_base_address($baseaddress);
$params && $self->url_params($params);
$db && $self->db($db);
$ret_type && $self->retrieval_type($ret_type);
$delay = $self->delay_policy unless defined $delay;
$self->delay($delay);
# insure we always have a default format set for retrieval
# even though this will be immedietly overwritten by most sub classes
$format = $self->default_format unless ( defined $format &&
$format ne '' );
$self->request_format($format);
my $ua = new LWP::UserAgent(env_proxy => 1);
$ua->agent(ref($self) ."/$MODVERSION");
$self->ua($ua);
$self->{'_authentication'} = [];
return $self;
}
# from Bio::DB::RandomAccessI
sub get_Seq_by_id {
my ($self,$seqid) = @_;
$self->_sleep;
my $seqio = $self->get_Stream_by_id([$seqid]);
$self->throw("id does not exist") if( !defined $seqio ) ;
if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) {
$self->warn("When complexity is set to 0, use get_Stream_by_id\n".
"Returning Bio::SeqIO object");
return $seqio;
}
my @seqs;
while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; }
$self->throw("id does not exist") unless @seqs;
if( wantarray ) { return @seqs } else { return shift @seqs }
}
sub get_Seq_by_acc {
my ($self,$seqid) = @_;
$self->_sleep;
my $seqio = $self->get_Stream_by_acc($seqid);
$self->throw("acc $seqid does not exist") if( ! defined $seqio );
if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) {
$self->warn("When complexity is set to 0, use get_Stream_by_acc\n".
"Returning Bio::SeqIO object");
return $seqio;
}
my @seqs;
while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; }
$self->throw("acc $seqid does not exist") unless @seqs;
if( wantarray ) { return @seqs } else { return shift @seqs }
}
sub get_Seq_by_gi {
my ($self,$seqid) = @_;
$self->_sleep;
my $seqio = $self->get_Stream_by_gi($seqid);
$self->throw("gi does not exist") if( !defined $seqio );
if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) {
$self->warn("When complexity is set to 0, use get_Stream_by_gi\n".
"Returning Bio::SeqIO object");
return $seqio;
}
my @seqs;
while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; }
$self->throw("gi does not exist") unless @seqs;
if( wantarray ) { return @seqs } else { return shift @seqs }
}
sub get_Seq_by_version {
my ($self,$seqid) = @_;
$self->_sleep;
my $seqio = $self->get_Stream_by_version($seqid);
$self->throw("accession.version does not exist") if( !defined $seqio );
if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) {
$self->warn("When complexity is set to 0, use get_Stream_by_version\n".
"Returning Bio::SeqIO object");
return $seqio;
}
my @seqs;
while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; }
$self->throw("accession.version does not exist") unless @seqs;
if( wantarray ) { return @seqs } else { return shift @seqs }
}
# implementing class must define these
sub get_request {
my ($self) = @_;
my $msg = "Implementing class must define method get_request in class WebDBSeqI";
$self->throw($msg);
}
# class methods
sub get_Stream_by_id {
my ($self, $ids) = @_;
my ($webfmt,$localfmt) = $self->request_format;
return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single',
'-format' => $webfmt);
}
*get_Stream_by_batch = sub {
my $self = shift;
$self->deprecated('get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead');
$self->get_Stream_by_id(@_)
};
sub get_Stream_by_acc {
my ($self, $ids ) = @_;
return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single');
}
sub get_Stream_by_gi {
my ($self, $ids ) = @_;
return $self->get_seq_stream('-uids' => $ids, '-mode' => 'gi');
}
sub get_Stream_by_version {
my ($self, $ids ) = @_;
# $self->throw("Implementing class should define this method!");
return $self->get_seq_stream('-uids' => $ids, '-mode' => 'version'); # how it should work
}
sub get_Stream_by_query {
my ($self, $query ) = @_;
return $self->get_seq_stream('-query' => $query, '-mode'=>'query');
}
sub default_format {
return $DEFAULTFORMAT;
}
# sorry, but this is hacked in because of BioFetch problems...
sub db {
my $self = shift;
my $d = $self->{_db};
$self->{_db} = shift if @_;
$d;
}
sub request_format {
my ($self, $value) = @_;
if( defined $value ) {
$self->{'_format'} = [ $value, $value];
}
return @{$self->{'_format'}};
}
sub get_seq_stream {
my ($self, %qualifiers) = @_;
my ($rformat, $ioformat) = $self->request_format();
my $seen = 0;
foreach my $key ( keys %qualifiers ) {
if( $key =~ /format/i ) {
$rformat = $qualifiers{$key};
$seen = 1;
}
}
$qualifiers{'-format'} = $rformat if( !$seen);
($rformat, $ioformat) = $self->request_format($rformat);
# These parameters are implemented for Bio::DB::GenBank objects only
if($self->isa('Bio::DB::GenBank')) {
$self->seq_start() && ($qualifiers{'-seq_start'} = $self->seq_start());
$self->seq_stop() && ($qualifiers{'-seq_stop'} = $self->seq_stop());
$self->strand() && ($qualifiers{'-strand'} = $self->strand());
defined $self->complexity() && ($qualifiers{'-complexity'} = $self->complexity());
}
my $request = $self->get_request(%qualifiers);
$request->proxy_authorization_basic($self->authentication)
if ( $self->authentication);
$self->debug("request is ". $request->as_string(). "\n");
# workaround for MSWin systems
$self->retrieval_type('io_string') if $self->retrieval_type =~ /pipeline/ && $^O =~ /^MSWin/;
if ($self->retrieval_type =~ /pipeline/) {
# Try to create a stream using POSIX fork-and-pipe facility.
# this is a *big* win when fetching thousands of sequences from
# a web database because we can return the first entry while
# transmission is still in progress.
# Also, no need to keep sequence in memory or in a temporary file.
# If this fails (Windows, MacOS 9), we fall back to non-pipelined access.
# fork and pipe: _stream_request()=><STREAM>
my ($result,$stream) = $self->_open_pipe();
if (defined $result) {
$DB::fork_TTY = File::Spec->devnull; # prevents complaints from debugge
if (!$result) { # in child process
$self->_stream_request($request,$stream);
POSIX::_exit(0); #prevent END blocks from executing in this forked child
}
else {
return Bio::SeqIO->new('-verbose' => $self->verbose,
'-format' => $ioformat,
'-fh' => $stream);
}
}
else {
$self->retrieval_type('io_string');
}
}
if ($self->retrieval_type =~ /temp/i) {
my $dir = $self->io->tempdir( CLEANUP => 1);
my ( $fh, $tmpfile) = $self->io()->tempfile( DIR => $dir );
close $fh;
my $resp = $self->_request($request, $tmpfile);
if( ! -e $tmpfile || -z $tmpfile || ! $resp->is_success() ) {
$self->throw("WebDBSeqI Error - check query sequences!\n");
}
$self->postprocess_data('type' => 'file',
'location' => $tmpfile);
# this may get reset when requesting batch mode
($rformat,$ioformat) = $self->request_format();
if( $self->verbose > 0 ) {
open(my $ERR, "<", $tmpfile);
while(<$ERR>) { $self->debug($_);}
}
return Bio::SeqIO->new('-verbose' => $self->verbose,
'-format' => $ioformat,
'-file' => $tmpfile);
}
if ($self->retrieval_type =~ /io_string/i ) {
my $resp = $self->_request($request);
my $content = $resp->content_ref;
$self->debug( "content is $$content\n");
if (!$resp->is_success() || length($$content) == 0) {
$self->throw("WebDBSeqI Error - check query sequences!\n");
}
($rformat,$ioformat) = $self->request_format();
$self->postprocess_data('type'=> 'string',
'location' => $content);
$self->debug( "str is $$content\n");
return Bio::SeqIO->new('-verbose' => $self->verbose,
'-format' => $ioformat,
'-fh' => new IO::String($$content));
}
# if we got here, we don't know how to handle the retrieval type
$self->throw("retrieval type " . $self->retrieval_type .
" unsupported\n");
}
sub url_base_address {
my $self = shift;
my $d = $self->{'_baseaddress'};
$self->{'_baseaddress'} = shift if @_;
$d;
}
sub proxy {
my ($self,$protocol,$proxy,$username,$password) = @_;
return if ( !defined $self->ua || !defined $protocol
|| !defined $proxy );
$self->authentication($username, $password)
if ($username && $password);
return $self->ua->proxy($protocol,$proxy);
}
sub authentication{
my ($self,$u,$p) = @_;
if( defined $u && defined $p ) {
$self->{'_authentication'} = [ $u,$p];
}
return @{$self->{'_authentication'}};
}
sub retrieval_type {
my ($self, $value) = @_;
if( defined $value ) {
$value = lc $value;
if( ! $RETRIEVAL_TYPES{$value} ) {
$self->warn("invalid retrieval type $value must be one of (" .
join(",", keys %RETRIEVAL_TYPES), ")");
$value = $DEFAULT_RETRIEVAL_TYPE;
}
$self->{'_retrieval_type'} = $value;
}
return $self->{'_retrieval_type'};
}
sub url_params {
my ($self, $value) = @_;
if( defined $value ) {
$self->{'_urlparams'} = $value;
}
}
sub ua {
my ($self, $ua) = @_;
if( defined $ua && $ua->isa("LWP::UserAgent") ) {
$self->{'_ua'} = $ua;
}
return $self->{'_ua'};
}
sub postprocess_data {
my ( $self, %args) = @_;
return;
}
# private methods
sub _request {
my ($self, $url,$tmpfile) = @_;
my ($resp);
if( defined $tmpfile && $tmpfile ne '' ) {
$resp = $self->ua->request($url, $tmpfile);
} else {
$resp = $self->ua->request($url);
}
if( $resp->is_error ) {
$self->throw("WebDBSeqI Request Error:\n".$resp->as_string);
}
return $resp;
}
#mod_perl-safe replacement for the open(BLEH,'-|') call. if running
#under mod_perl, detects it and closes the child's STDIN and STDOUT
#handles
sub _open_pipe {
my ($self) = @_;
# is mod_perl running? Which API?
my $mp = $self->mod_perl_api;
if($mp and ! our $loaded_apache_sp) {
my $load_api = ($mp == 1) ? 'use Apache::SubProcess': 'use Apache2::SubProcess';
eval $load_api;
$@ and $self->throw("$@\n$load_api module required for running under mod_perl");
$loaded_apache_sp = 1;
}
my $pipe = IO::Pipe->new();
local $SIG{CHLD} = 'IGNORE';
defined(my $pid = fork)
or $self->throw("Couldn't fork: $!");
unless($pid) {
#CHILD
$pipe->writer();
#if we're running under mod_perl, clean up some things after this fork
if ($ENV{MOD_PERL} and my $r = eval{Apache->request} ) {
$r->cleanup_for_exec;
#don't read or write the mod_perl parent's tied filehandles
close STDIN; close STDOUT;
setsid() or $self->throw('Could not detach from parent');
}
} else {
#PARENT
$pipe->reader();
}
return ( $pid, $pipe );
}
# send web request to specified filehandle, or stdout, for streaming purposes
sub _stream_request {
my $self = shift;
my $request = shift;
my $dest_fh = shift || \*STDOUT;
# fork so as to pipe output of fetch process through to
# postprocess_data method call.
my ($child,$fetch) = $self->_open_pipe();
if ($child) {
#PARENT
local ($/) = "//\n"; # assume genbank/swiss format
$| = 1;
my $records = 0;
while (my $record = <$fetch>) {
$records++;
$self->postprocess_data('type' => 'string',
'location' => \$record);
print $dest_fh $record;
}
$/ = "\n"; # reset to be safe;
close $dest_fh; #must explicitly close here, because the hard
#exits don't cloes them for us
}
else {
#CHILD
$| = 1;
my $resp = $self->ua->request($request,
sub { print $fetch $_[0] }
);
if( $resp->is_error ) {
$self->throw("WebDBSeqI Request Error:\n".$resp->as_string);
}
close $fetch; #must explicitly close here, because the hard exists
#don't close them for us
POSIX::_exit(0);
}
}
sub io {
my ($self,$io) = @_;
if(defined($io) || (! exists($self->{'_io'}))) {
$io = Bio::Root::IO->new() unless $io;
$self->{'_io'} = $io;
}
return $self->{'_io'};
}
sub delay {
my $self = shift;
my $d = $self->{'_delay'};
$self->{'_delay'} = shift if @_;
$d;
}
sub delay_policy {
my $self = shift;
return 0;
}
sub _sleep {
my $self = shift;
my $last_invocation = $LAST_INVOCATION_TIME;
if (time - $LAST_INVOCATION_TIME < $self->delay) {
my $delay = $self->delay - (time - $LAST_INVOCATION_TIME);
warn "sleeping for $delay seconds\n" if $self->verbose > 0;
sleep $delay;
}
$LAST_INVOCATION_TIME = time;
}
sub mod_perl_api {
my $self = shift;
my $v = $ENV{MOD_PERL} ?
( exists $ENV{MOD_PERL_API_VERSION} && $ENV{MOD_PERL_API_VERSION} >= 2 ) ?
2 :
1
: 0;
return $v;
}
1;