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Summary

Bio::DB::NCBIHelper - A collection of routines useful for queries to
NCBI databases.

Package variables

Included modules

Inherit

Bio::DB::WebDBSeqI Bio::Root::Root

Synopsis

 # Do not use this module directly.

 # get a Bio::DB::NCBIHelper object somehow
 my $seqio = $db->get_Stream_by_acc(['MUSIGHBA1']);
 foreach my $seq ( $seqio->next_seq ) {
     # process seq
 }

Description

Provides a single place to setup some common methods for querying NCBI
web databases. This module just centralizes the methods for
constructing a URL for querying NCBI GenBank and NCBI GenPept and the
common HTML stripping done in postprocess_data().
The base NCBI query URL used is:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi

Methods

Methods description

 Title   : get_params
 Usage   : my %params = $self->get_params($mode)
 Function: Returns key,value pairs to be passed to NCBI database
           for either 'batch' or 'single' sequence retrieval method
 Returns : a key,value pair hash
 Args    : 'single' or 'batch' mode for retrieval

 Title   : default_format
 Usage   : my $format = $self->default_format
 Function: Returns default sequence format for this module
 Returns : string
 Args    : none

 Title   : get_request
 Usage   : my $url = $self->get_request
 Function: HTTP::Request
 Returns : 
 Args    : %qualifiers = a hash of qualifiers (ids, format, etc)

  Title   : get_Stream_by_batch
  Usage   : $seq = $db->get_Stream_by_batch($ref);
  Function: Retrieves Seq objects from Entrez 'en masse', rather than one
            at a time.  For large numbers of sequences, this is far superior
            than get_Stream_by_[id/acc]().
  Example :
  Returns : a Bio::SeqIO stream object
  Args    : $ref : either an array reference, a filename, or a filehandle
            from which to get the list of unique ids/accession numbers.

  Title   : get_Stream_by_query
  Usage   : $seq = $db->get_Stream_by_query($query);
  Function: Retrieves Seq objects from Entrez 'en masse', rather than one
            at a time.  For large numbers of sequences, this is far superior
            than get_Stream_by_[id/acc]().
  Example :
  Returns : a Bio::SeqIO stream object
  Args    : $query :   An Entrez query string or a
            Bio::DB::Query::GenBank object.  It is suggested that you
            create a Bio::DB::Query::GenBank object and get the entry
            count before you fetch a potentially large stream.

 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

 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

 Title   : redirect_refseq
 Usage   : $db->redirect_refseq(1)
 Function: simple getter/setter which redirects RefSeqs to use Bio::DB::RefSeq
 Returns : Boolean value
 Args    : Boolean value (optional)
 Throws  : 'unparseable output exception'
 Note    : This replaces 'no_redirect' as a more straightforward flag to
           redirect possible RefSeqs to use Bio::DB::RefSeq (EBI interface)
           instead of retrievign the NCBI records

 Title   : complexity
 Usage   : $db->complexity(3)
 Function: get/set complexity value 
 Returns : value from 0-4 indicating level of complexity
 Args    : value from 0-4 (optional); if unset server assumes 1
 Throws  : if arg is not an integer or falls outside of noted range above
 Note    : From efetch docs:

    Complexity regulates the display:

       * 0 - get the whole blob
       * 1 - get the bioseq for gi of interest (default in Entrez)
       * 2 - get the minimal bioseq-set containing the gi of interest
       * 3 - get the minimal nuc-prot containing the gi of interest
       * 4 - get the minimal pub-set containing the gi of interest

 Title   : strand
 Usage   : $db->strand(1)
 Function: get/set strand value 
 Returns : strand value if set
 Args    : value of 1 (plus) or 2 (minus); if unset server assumes 1
 Throws  : if arg is not an integer or is not 1 or 2
 Note    : This differs from BioPerl's use of strand: 1 = plus, -1 = minus 0 = not relevant.
           We should probably add in some functionality to convert over in the future.

 Title   : seq_start
 Usage   : $db->seq_start(123)
 Function: get/set sequence start location
 Returns : sequence start value if set
 Args    : integer; if unset server assumes 1
 Throws  : if arg is not an integer

 Title   : seq_stop
 Usage   : $db->seq_stop(456)
 Function: get/set sequence stop (end) location
 Returns : sequence stop (end) value if set
 Args    : integer; if unset server assumes 1
 Throws  : if arg is not an integer

  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()

  Title   : _check_id
  Usage   : 
  Function: 
  Returns : A Bio::DB::RefSeq reference or throws
  Args    : $id(s), $string

  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: NCBI requests a delay of 3 seconds between requests.  This method
        implements that policy.

 Title   : cookie
 Usage   : ($cookie,$querynum) = $db->cookie
 Function: return the NCBI query cookie
 Returns : list of (cookie,querynum)
 Args    : none

 Title   : _parse_response
 Usage   : $db->_parse_response($content)
 Function: parse out response for cookie
 Returns : empty
 Args    : none
 Throws  : 'unparseable output exception'

 Title   : no_redirect
 Usage   : $db->no_redirect($content)
 Function: Used to indicate that Bio::DB::GenBank instance retrieves
           possible RefSeqs from EBI instead; default behavior is now to
           retrieve directly from NCBI
 Returns : None
 Args    : None
 Throws  : Method is deprecated in favor of positive flag method 'redirect_refseq'

Methods code

BEGIN {

    $MAX_ENTRIES = 19000;
    $HOSTBASE = 'http://eutils.ncbi.nlm.nih.gov';
    %CGILOCATION = (
			'batch'  => ['post' => '/entrez/eutils/epost.fcgi'],
		    'query'  => ['get'  => '/entrez/eutils/efetch.fcgi'],
		    'single' => ['get'  => '/entrez/eutils/efetch.fcgi'],
		    'version'=> ['get'  => '/entrez/eutils/efetch.fcgi'],
		    'gi'   =>   ['get'  => '/entrez/eutils/efetch.fcgi'],
			'webenv' => ['get'  => '/entrez/eutils/efetch.fcgi']
		     );

    %FORMATMAP = ( 'gb' => 'genbank',
						   'gp' => 'genbank',
						   'fasta' => 'fasta',
						   'asn.1' => 'entrezgene',
						   'gbwithparts' => 'genbank',
					  );
    $DEFAULTFORMAT = 'gb';

}

sub new {

    my ($class, @args ) = @_;
    my $self = $class->SUPER::new(@args);
    my ($seq_start,$seq_stop,$no_redirect, $redirect, $complexity,$strand) =
	 $self->_rearrange([qw(SEQ_START SEQ_STOP NO_REDIRECT REDIRECT_REFSEQ COMPLEXITY STRAND)],
							 @args);
	$seq_start     && $self->seq_start($seq_start);
    $seq_stop      && $self->seq_stop($seq_stop);
    $no_redirect   && $self->no_redirect($no_redirect);
    $redirect      && $self->redirect_refseq($redirect);
    $strand        && $self->strand($strand);
	# adjust statement to accept zero value
	defined $complexity && ($complexity >=0 && $complexity <=4)
		&& $self->complexity($complexity);
    return $self;

}

sub get_params {

    my ($self, $mode) = @_;
    $self->throw("subclass did not implement get_params");

}

sub default_format {

    return $DEFAULTFORMAT;

}

sub get_request {

	my ($self, @qualifiers) = @_;
	my ($mode, $uids, $format, $query, $seq_start, $seq_stop, $strand, $complexity) = 
	  $self->_rearrange([qw(MODE UIDS FORMAT QUERY SEQ_START SEQ_STOP STRAND COMPLEXITY)],
							  @qualifiers);
	$mode = lc $mode;
	($format) = $self->request_format() unless ( defined $format);
	if( !defined $mode || $mode eq '' ) { $mode = 'single'; }
	my %params = $self->get_params($mode);
	if( ! %params ) {
		$self->throw("must specify a valid retrieval mode 'single' or 'batch' not '$mode'") 
	}
	my $url = URI->new($HOSTBASE . $CGILOCATION{$mode}[1]);
	unless( $mode eq 'webenv' || defined $uids || defined $query) {
		$self->throw("Must specify a query or list of uids to fetch");
	}
	if ($query && $query->can('cookie')) {
		@params{'WebEnv','query_key'} = $query->cookie;
		$params{'db'}                 = $query->db;
	}
	elsif ($query) {
		$params{'id'} = join ',',$query->ids;
	}
	# for batch retrieval, non-query style
	elsif ($mode eq 'webenv' && $self->can('cookie')) {
		@params{'WebEnv','query_key'} = $self->cookie;
	}
	elsif ($uids) {
		if( ref($uids) =~ /array/i ) {
			$uids = join(",", @$uids);
		}
		$params{'id'}      = $uids;
	}
	$seq_start && ($params{'seq_start'} = $seq_start);
	$seq_stop && ($params{'seq_stop'} = $seq_stop);
	$strand && ($params{'strand'} = $strand);
	if (defined $complexity && ($seq_start || $seq_stop || $strand)) {
		$self->warn("Complexity set to $complexity; seq_start and seq_stop may not work!")
			if ($complexity != 1 && ($seq_start || $seq_stop));
		$self->warn("Complexity set to 0; expect strange results with strand set to 2")
			if ($complexity == 0 && $strand == 2 && $format eq 'fasta');
	}
	defined $complexity && ($params{'complexity'} = $complexity);
	$params{'rettype'} = $format unless $mode eq 'batch';
	# for now, 'post' is batch retrieval
	if ($CGILOCATION{$mode}[0] eq 'post') {
		my $response = $self->ua->request(POST $url,[%params]);
		$response->proxy_authorization_basic($self->authentication)
			if ( $self->authentication);
		$self->_parse_response($response->content);
		my ($cookie, $querykey) = $self->cookie;
		my %qualifiers = ('-mode' 			=> 'webenv',
						  '-seq_start' 		=> $seq_start,
						  '-seq_stop' 		=> $seq_stop,
						  '-strand'			=> $strand,
						  '-complexity'		=> $complexity,
						  '-format'			=> $format);
		return $self->get_request(%qualifiers);
	} else {
		$url->query_form(%params);
		return GET $url;
	}

}

sub get_Stream_by_batch {

    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_query {

    my ($self, $query) = @_;
    unless (ref $query && $query->can('query')) {
       $query = Bio::DB::Query::GenBank->new($query);
    }
    return $self->get_seq_stream('-query' => $query, '-mode'=>'query');

}

sub postprocess_data {

	# retain this in case postprocessing is needed at a future date

}

sub request_format {

	my ($self, $value) = @_;    
	if( defined $value ) {
		$value = lc $value;	
		if( defined $FORMATMAP{$value} ) {
			$self->{'_format'} = [ $value, $FORMATMAP{$value}];
		} else {
			# Try to fall back to a default. Alternatively, we could throw
			# an exception
			$self->{'_format'} = [ $value, $value ];
		}
	}
	return @{$self->{'_format'}};

}

sub redirect_refseq {

    my $self = shift;
    return $self->{'_redirect_refseq'} = shift if @_;
    return $self->{'_redirect_refseq'};

}

sub complexity {

    my ($self, $comp) = @_;
    if (defined $comp) {
        $self->throw("Complexity value must be integer between 0 and 4") if
            $comp !~ /^\d+$/ || $comp < 0 || $comp > 4;
        $self->{'_complexity'} = $comp;
    }
    return $self->{'_complexity'};

}

sub strand {

    my ($self, $str) = @_;
    if ($str) {
        $self->throw("strand() must be integer value of 1 (plus strand) or 2 (minus strand) if set") if
            $str !~ /^\d+$/ || $str < 1 || $str > 2;
        $self->{'_strand'} = $str;
    }
    return $self->{'_strand'};

}

sub seq_start {

    my ($self, $start) = @_;
    if ($start) {
        $self->throw("seq_start() must be integer value if set") if
            $start !~ /^\d+$/;
        $self->{'_seq_start'} = $start;
    }
    return $self->{'_seq_start'};

}

sub seq_stop {

    my ($self, $stop) = @_;
    if ($stop) {
        $self->throw("seq_stop() must be integer if set") if
            $stop !~ /^\d+$/;
        $self->{'_seq_stop'} = $stop;
    }
    return $self->{'_seq_stop'};

}

sub get_Stream_by_acc {

    my ($self, $ids ) = @_;
    my $newdb = $self->_check_id($ids);
    if (defined $newdb && ref($newdb) && $newdb->isa('Bio::DB::RefSeq')) {
	return $newdb->get_seq_stream('-uids' => $ids, '-mode' => 'single');
    } else {
	return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single');
    }

}

sub _check_id {

	my ($self, $ids) = @_;

	# NT contigs can not be retrieved
	$self->throw("NT_ contigs are whole chromosome files which are not part of regular".
					 "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") 
	  if $ids =~ /NT_/;

	# Asking for a RefSeq from EMBL/GenBank
   
	if ($self->redirect_refseq) {
		if ($ids =~ /N._/) {
			$self->warn("[$ids] is not a normal sequence database but a RefSeq entry.".
							" Redirecting the request.\n")
			  if $self->verbose >= 0;
			return  Bio::DB::RefSeq->new();
		}
	}

}

sub delay_policy {

  my $self = shift;
  return 3;

}

sub cookie {

  my $self = shift;
  if (@_) {
    $self->{'_cookie'}   = shift;
    $self->{'_querynum'} = shift;
  }
  else {
    return @{$self}{qw(_cookie _querynum)};
  }

}

sub _parse_response {

  my $self    = shift;
  my $content = shift;
  if (my ($warning) = $content =~ m!<ErrorList>(.+)</ErrorList>!s) {
    $self->warn("Warning(s) from GenBank: $warning\n");
  }
  if (my ($error) = $content =~ /<OutputMessage>([^<]+)/) {
    $self->throw("Error from Genbank: $error");
  }
  my ($cookie)    = $content =~ m!<WebEnv>(\S+)</WebEnv>!;
  my ($querykey)  = $content =~ m!<QueryKey>(\d+)!;
  $self->cookie(uri_unescape($cookie),$querykey);
}

########### DEPRECATED!!!! ###########

}

sub no_redirect {

    shift->throw(
    "Use of no_redirect() is deprecated.  Bio::DB::GenBank default is to always\n".
    "retrieve from NCBI.  In order to redirect possible RefSeqs to EBI, set\n".
    "redirect_refseq flag to 1");
}

1;

__END__

}

General documentation

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
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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.

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/

Email jason@bioperl.org

The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _

Overriding WebDBSeqI method to help newbies to retrieve sequences