#
# BioPerl module for Bio::DB::NCBIHelper
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
# Interfaces with new WebDBSeqI interface
=head1 NAME
Bio::DB::NCBIHelper - A collection of routines useful for queries to
NCBI databases.
=head1 SYNOPSIS
# Do not use this module directly.
# get a Bio::DB::NCBIHelper object somehow
my $seqio = $db->get_Stream_by_acc(['J00522']);
foreach my $seq ( $seqio->next_seq ) {
# process seq
}
=head1 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 L<postprocess_data>().
The base NCBI query URL used is:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
=cut
# Let the code begin...
package Bio::DB::NCBIHelper;
use strict;
use Bio::DB::Query::GenBank;
use HTTP::Request::Common;
use URI;
use Bio::Root::IO;
use Bio::DB::RefSeq;
use URI::Escape qw(uri_unescape);
use base qw(Bio::DB::WebDBSeqI Bio::Root::Root);
our $HOSTBASE = 'http://eutils.ncbi.nlm.nih.gov';
our $MAX_ENTRIES = 19000;
our $REQUEST_DELAY = 3;
our %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' ]
);
our %FORMATMAP = (
'gb' => 'genbank',
'gp' => 'genbank',
'fasta' => 'fasta',
'asn.1' => 'entrezgene',
'gbwithparts' => 'genbank',
);
our $DEFAULTFORMAT = 'gb';
=head2 new
Title : new
Usage :
Function: the new way to make modules a little more lightweight
Returns :
Args :
=cut
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;
}
=head2 get_params
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
=cut
sub get_params {
my ($self, $mode) = @_;
$self->throw("subclass did not implement get_params");
}
=head2 default_format
Title : default_format
Usage : my $format = $self->default_format
Function: returns default sequence format for this module
Returns : string
Args : none
=cut
sub default_format {
return $DEFAULTFORMAT;
}
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
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;
}
}
=head2 get_Stream_by_batch
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 or get_Stream_by_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.
NOTE: deprecated API. Use get_Stream_by_id() instead.
=cut
*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(@_)
};
=head2 get_Stream_by_query
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
to get_Stream_by_id and get_Stream_by_acc.
Example :
Returns : a Bio::SeqIO stream object
Args : 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.
=cut
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');
}
=head2 postprocess_data
Title : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr );
Function: Process downloaded data before loading into a Bio::SeqIO. This
works for Genbank and Genpept, other classes should override
it with their own method.
Returns : void
Args : hash with two keys:
'type' can be 'string' or 'file'
'location' either file location or string reference containing data
=cut
sub postprocess_data {
# retain this in case postprocessing is needed at a future date
}
=head2 request_format
Title : request_format
Usage : my ($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
=cut
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'} };
}
=head2 redirect_refseq
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 retrieving the NCBI records
=cut
sub redirect_refseq {
my $self = shift;
return $self->{'_redirect_refseq'} = shift if @_;
return $self->{'_redirect_refseq'};
}
=head2 complexity
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, the 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
=cut
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'};
}
=head2 strand
Title : strand
Usage : $db->strand(1)
Function: get/set strand value
Returns : strand value if set
Args : value of 1 (plus) or 2 (minus); if unset server assumes 1
Throws : if arg is not an integer or is not 1 or 2
Note : This differs from BioPerl's use of strand: 1 = plus, -1 = minus 0 = not relevant.
We should probably add in some functionality to convert over in the future.
=cut
sub strand {
my ($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'};
}
=head2 seq_start
Title : seq_start
Usage : $db->seq_start(123)
Function: get/set sequence start location
Returns : sequence start value if set
Args : integer; if unset server assumes 1
Throws : if arg is not an integer
=cut
sub seq_start {
my ($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'};
}
=head2 seq_stop
Title : seq_stop
Usage : $db->seq_stop(456)
Function: get/set sequence stop (end) location
Returns : sequence stop (end) value if set
Args : integer; if unset server assumes 1
Throws : if arg is not an integer
=cut
sub seq_stop {
my ($self, $stop) = @_;
if ($stop) {
$self->throw("seq_stop() must be integer if set") if
$stop !~ /^\d+$/;
$self->{'_seq_stop'} = $stop;
}
return $self->{'_seq_stop'};
}
=head2 Bio::DB::WebDBSeqI methods
Overriding WebDBSeqI method to help newbies to retrieve sequences
=head2 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()
=cut
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' );
}
}
=head2 _check_id
Title : _check_id
Usage :
Function:
Returns : a Bio::DB::RefSeq reference or throws
Args : $id(s), $string
=cut
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();
}
}
}
=head2 delay_policy
Title : delay_policy
Usage : $secs = $self->delay_policy
Function: NCBI requests a delay of 3 seconds between requests. This method
implements that policy.
Returns : number of seconds to delay
Args : none
=cut
sub delay_policy {
my $self = shift;
return $REQUEST_DELAY;
}
=head2 cookie
Title : cookie
Usage : ($cookie,$querynum) = $db->cookie
Function: return the NCBI query cookie, this information is used by
Bio::DB::GenBank in conjunction with efetch, ripped from
Bio::DB::Query::GenBank
Returns : list of (cookie,querynum)
Args : none
=cut
sub cookie {
my $self = shift;
if (@_) {
$self->{'_cookie'} = shift;
$self->{'_querynum'} = shift;
}
else {
return @{$self}{qw(_cookie _querynum)};
}
}
=head2 _parse_response
Title : _parse_response
Usage : $db->_parse_response($content)
Function: parse out response for cookie, this is a trimmed-down version
of _parse_response from Bio::DB::Query::GenBank
Returns : empty
Args : none
Throws : 'unparseable output exception'
=cut
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 );
}
=head2 no_redirect
Title : no_redirect
Usage : $db->no_redirect($content)
Function: DEPRECATED - 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'
=cut
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__