SYNOPSIS
my $eutil = Bio::DB::EUtilities->new(
-eutil => 'esearch',
-term => 'BRCA1',
-db => 'pubmed',
-retmax => 10000,
-email => '[email protected]'); # please use your real email
# eutil => any of esearch, esummary, elink
@ids = $eutil->get_ids(); # returns array or array ref of IDs
# eutil => any of egquery, espell
$term = $eutil->get_term(); # returns array or array ref of IDs
# eutil => any of elink, einfo
$db = $eutil->get_database(); # returns database
# Query-related methods (esearch, egquery, espell data)
# eutil data centered on use of search terms
my $ct = $eutil->get_count; # uses optional database for egquery count
my $translation = $eutil->get_count;
my $corrected = $eutil->get_corrected_query; # espell
while (my $gquery = $eutil->next_GlobalQuery) {
# iterates through egquery data
}
# Info-related methods (einfo data)
# database-related information
my $desc = $eutil->get_description;
my $update = $eutil->get_last_update;
my $nm = $eutil->get_menu_name;
my $ct = $eutil->get_record_count;
while (my $field = $eutil->next_FieldInfo) {
# ...
}
while (my $field = $eutil->next_LinkInfo) {
# ...
}
# History methods (epost data, some data returned from elink)
# data which enables one to retrieve and query against user-stored
# information on the NCBI server
while (my $cookie = $eutil->next_History) {
# ...
}
my @hists = $eutil->get_Histories;
# Bio::Tools::EUtilities::Summary (esummary data)
# information on a specific database record
# retrieve nested docsum data
while (my $docsum = $eutil->next_DocSum) {
print "ID:",$docsum->get_ids,"\n";
while (my $item = $docsum->next_Item) {
# do stuff here...
while (my $listitem = $docsum->next_ListItem) {
# do stuff here...
while (my $listitem = $docsum->next_Structure) {
# do stuff here...
}
}
}
}
# retrieve flattened item list per DocSum
while (my $docsum = $eutil->next_DocSum) {
my @items = $docsum->get_all_DocSum_Items;
}
DESCRIPTION
This is a general webagent which posts and retrieves data to NCBI's eUtils service using their CGI interface. A separate project, currently present in BioPerl-Run, utilizes the SOAP-based interface for eUtils.A full explanation of the eUtils interfaces are not possible within this short module; please see the BioPerl wiki HOWTO for more details.
TODO
-
Finish documentation
HOWTOs (both standard and Cookbook).
-
Cookbook tests
Set up dev-only tests for Cookbook examples to make sure they are consistently updated.
-
API
Mark Jensen has written up the SOAP-based eUtil modules, maybe we should coalesce around a consistent API between the two (they are close).
-
Carryover of parameters
Maybe add a default but configurable list of parameters that can be carried over between calls.
-
Make setting certain parameters consistent
Setting history is a bit inconsistent, so maybe use a common alias for this?
-
Splitting out of core
This could easily belong in its own distribution, the only tie to BioPerl is the use of Bio::Root::Root.
-
Moosify?
Not necessary, but it might make things easier and more maintainable in the long run.
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.
[email protected] - General discussion http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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
Email cjfields at bioperl dot orgAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _Bio::DB::GenericWebAgent methods
GenericWebDBI methods
parameter_base
Title : parameter_base Usage : $dbi->parameter_base($pobj); Function: Get/Set Bio::ParameterBaseI. Returns : Bio::ParameterBaseI object Args : Bio::ParameterBaseI object
ua
Title : ua Usage : $dbi->ua; Function: Get/Set LWP::UserAgent. Returns : LWP::UserAgent Args : LWP::UserAgent
get_Response
Title : get_Response
Usage : $agent->get_Response;
Function: Get the HTTP::Response object by passing it an HTTP::Request (generated from
Bio::ParameterBaseI implementation).
Returns : HTTP::Response object or data if callback is used
Args : (optional)
-cache_response - flag to cache HTTP::Response object;
Default is 1 (TRUE, caching ON)
These are passed on to LWP::UserAgent::request() if stipulated
-cb - use a LWP::UserAgent-compliant callback
-file - dumps the response to a file (handy for large responses)
Note: can't use file and callback at the same time
-read_size_hint - bytes of content to read in at a time to pass to callback
Note : Caching and parameter checking are set
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.
LWP::UserAgent related methods
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
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: NCBI requests a delay of 3 requests per second. This method implements that policy. This will likely change to check time of day or number of requests for lengthening delays.
get_Parser
Title : get_Parser
Usage : $agent->get_Parser;
Function: Retrieve the parser used for last agent request
Returns : The Bio::Tools::EUtilities parser used to parse the HTTP::Response
content
Args : None
Note : Abstract method; defined by implementation
Bio::Tools::EUtilities::EUtilParameters-delegating methods
This is only a subset of parameters available from Bio::Tools::EUtilities::EUtilParameters (the ones deemed absolutely necessary). All others are available by calling 'parameter_base->method' when needed.set_parameters
Title : set_parameters
Usage : $pobj->set_parameters(@params);
Function: sets the NCBI parameters listed in the hash or array
Returns : None
Args : [optional] hash or array of parameter/values.
Note : This sets any parameter (i.e. doesn't screen them). In addition to
regular eutil-specific parameters, you can set the following:
-eutil - the eUtil to be used (default 'efetch')
-history - pass a HistoryI-implementing object, which
sets the WebEnv, query_key, and possibly db and linkname
(the latter two only for LinkSets)
-correspondence - Boolean flag, set to TRUE or FALSE; indicates how
IDs are to be added together for elink request where
ID correspondence might be needed
(default 0)
reset_parameters
Title : reset_parameters
Usage : resets values
Function: resets parameters to either undef or value in passed hash
Returns : none
Args : [optional] hash of parameter-value pairs
Note : this also resets eutil(), correspondence(), and the history and request
cache
available_parameters
Title : available_parameters
Usage : @params = $pobj->available_parameters()
Function: Returns a list of the available parameters
Returns : Array of available parameters (no values)
Args : [optional] A string; either eutil name (for returning eutil-specific
parameters) or 'history' (for those parameters allowed when retrieving
data stored on the remote server using a 'History' object).
get_parameters
Title : get_parameters
Usage : @params = $pobj->get_parameters;
%params = $pobj->get_parameters;
Function: Returns list of key/value pairs, parameter => value
Returns : Flattened list of key-value pairs. All key-value pairs returned,
though subsets can be returned based on the '-type' parameter.
Data passed as an array ref are returned based on whether the
'-join_id' flag is set (default is the same array ref).
Args : -type : the eutil name or 'history', for returning a subset of
parameters (Default: returns all)
-join_ids : Boolean; join IDs based on correspondence (Default: no join)
get_parameter_values
Title : get_parameter_values
Usage : @vals = $factory->get_parameter_value('id'); # always get array
Function: Returns the specific parameter values.
Returns : For consistency returns a list of values for this parameter. If only
one is expected, use:
($val) = $factory->get_parameter_value('id');
Args : parameter expected
Bio::Tools::EUtilities-delegating methods
Bio::Tools::EUtilities::EUtilDataI methods
eutil
Title : eutil Usage : $eutil->$foo->eutil Function : Get/Set eutil Returns : string Args : string (eutil) Throws : on invalid eutil
datatype
Title : datatype Usage : $type = $foo->datatype; Function : Get/Set data object type Returns : string Args : string
to_string
Title : to_string Usage : $foo->to_string() Function : converts current object to string Returns : none Args : (optional) simple data for text formatting Note : Implemented in plugins
print_all
Title : print_all
Usage : $info->print_all();
$info->print_all(-fh => $fh, -cb => $coderef);
Function : prints (dumps) all data in parser. Unless a coderef is supplied,
this just dumps the parser-specific to_string method to either a
file/fh or STDOUT
Returns : none
Args : [optional]
-file : file to print to
-fh : filehandle to print to (cannot be used concurrently with file)
-cb : coderef to use in place of default print method. This is passed
in a LinkSet object
-wrap : number of columns to wrap default text output to (def = 80)
Notes : only applicable for einfo. If -file or -fh are not defined,
prints to STDOUT
Methods useful for multiple eutils
get_ids
Title : get_ids
Usage : my @ids = $parser->get_ids
Function : returns array of requested IDs (see Notes for more specifics)
Returns : array
Args : [conditional] not required except when running elink queries against
multiple databases. In case of the latter, the database name is
optional but recommended when retrieving IDs as the ID list will
be globbed together. In such cases, if a db name isn't provided a
warning is issued as a reminder.
Notes : esearch : returned ID list
elink : returned ID list (see Args above for caveats)
all others : from parameter_base->id or undef
get_database
Title : get_database
Usage : my $db = $info->get_database;
Function : returns single database name (eutil-compatible). This is the queried
database. For most eutils this is straightforward. For elinks
(which have 'db' and 'dbfrom') this is dbto, for egquery, it is the first
db in the list (you probably want get_databases instead)
Returns : string
Args : none
Notes : egquery : first db in the query (you probably want get_databases)
einfo : the queried database
espell : the queried database
elink : from parameter_base->dbfrom or undef
all others : from parameter_base->db or undef
get_db (alias for get_database)
get_databases
Title : get_databases
Usage : my @dbs = $parser->get_databases
Function : returns list of databases
Returns : array of strings
Args : none
Notes : This is guaranteed to return a list of databases. For a single
database use the convenience method get_db/get_database
egquery : list of all databases in the query
einfo : the queried database
espell : the queried database
all others : from parameter_base->db or undef
get_dbs (alias for get_databases)
next_History
Title : next_History
Usage : while (my $hist=$parser->next_History) {...}
Function : returns next HistoryI (if present).
Returns : Bio::Tools::EUtilities::HistoryI (Cookie or LinkSet)
Args : none
Note : esearch, epost, and elink are all capable of returning data which
indicates search results (in the form of UIDs) is stored on the
remote server. Access to this data is wrapped up in simple interface
(HistoryI), which is implemented in two classes:
Bio::DB::EUtilities::History (the simplest) and
Bio::DB::EUtilities::LinkSet. In general, calls to epost and esearch
will only return a single HistoryI object (formerly known as a
Cookie), but calls to elink can generate many depending on the
number of IDs, the correspondence, etc. Hence this iterator, which
allows one to retrieve said data one piece at a time.
next_cookie (alias for next_History)
get_Histories
Title : get_Histories Usage : my @hists = $parser->get_Histories Function : returns list of HistoryI objects. Returns : list of Bio::Tools::EUtilities::HistoryI (Cookie or LinkSet) Args : none
Query-related methods
get_count
Title : get_count
Usage : my $ct = $parser->get_count
Function : returns the count (hits for a search)
Returns : integer
Args : [CONDITIONAL] string with database name - used to retrieve
count from specific database when using egquery
Notes : egquery : count for specified database (specified above)
esearch : count for last search
all others : undef
get_term
Title : get_term
Usage : $st = $qd->get_term;
Function : retrieve the term for the global search
Returns : string
Args : none
Notes : egquery : search term
espell : search term
esearch : from parameter_base->term or undef
all others : undef
get_translation_from
Title : get_translation_from Usage : $string = $qd->get_translation_from(); Function: portion of the original query replaced with translated_to() Returns : string Args : none Note : only applicable for esearch
get_translation_to
Title : get_translation_to Usage : $string = $qd->get_translation_to(); Function: replaced string used in place of the original query term in translation_from() Returns : string Args : none Note : only applicable for esearch
get_retstart
Title : get_retstart
Usage : $start = $qd->get_retstart();
Function : retstart setting for the query (either set or NCBI default)
Returns : Integer
Args : none
Notes : esearch : retstart
esummary : retstart
all others : from parameter_base->retstart or undef
get_retmax
Title : get_retmax
Usage : $max = $qd->get_retmax();
Function : retmax setting for the query (either set or NCBI default)
Returns : Integer
Args : none
Notes : esearch : retmax
esummary : retmax
all others : from parameter_base->retmax or undef
get_query_translation
Title : get_query_translation
Usage : $string = $qd->get_query_translation();
Function: returns the translated query used for the search (if any)
Returns : string
Args : none
Notes : only applicable for esearch. This is the actual term used for
esearch.
get_corrected_query
Title : get_corrected_query Usage : my $cor = $eutil->get_corrected_query; Function : retrieves the corrected query when using espell Returns : string Args : none Notes : only applicable for espell.
get_replaced_terms
Title : get_replaced_terms Usage : my $term = $eutil->get_replaced_terms Function : returns array of strings replaced in the query Returns : string Args : none Notes : only applicable for espell
next_GlobalQuery
Title : next_GlobalQuery
Usage : while (my $query = $eutil->next_GlobalQuery) {...}
Function : iterates through the queries returned from an egquery search
Returns : GlobalQuery object
Args : none
Notes : only applicable for egquery
get_GlobalQueries
Title : get_GlobalQueries Usage : @queries = $eutil->get_GlobalQueries Function : returns list of GlobalQuery objects Returns : array of GlobalQuery objects Args : none Notes : only applicable for egquery
print_GlobalQueries
Title : print_GlobalQueries
Usage : $docsum->print_GlobalQueries();
$docsum->print_GlobalQueries(-fh => $fh, -cb => $coderef);
Function : prints item data for all global queries. The default printing
method is each item per DocSum is printed with relevant values if
present in a simple table using Text::Wrap.
Returns : none
Args : [optional]
-file : file to print to
-fh : filehandle to print to (cannot be used concurrently with file)
-cb : coderef to use in place of default print method. This is passed
in a GlobalQuery object;
-wrap : number of columns to wrap default text output to (def = 80)
Notes : only applicable for esummary. If -file or -fh are not defined,
prints to STDOUT
Summary-related methods
next_DocSum
Title : next_DocSum
Usage : while (my $ds = $esum->next_DocSum) {...}
Function : iterate through DocSum instances
Returns : single Bio::Tools::EUtilities::Summary::DocSum
Args : none yet
Notes : only applicable for esummary
get_DocSums
Title : get_DocSums Usage : my @docsums = $esum->get_DocSums Function : retrieve a list of DocSum instances Returns : array of Bio::Tools::EUtilities::Summary::DocSum Args : none Notes : only applicable for esummary
print_DocSums
Title : print_DocSums
Usage : $docsum->print_DocSums();
$docsum->print_DocSums(-fh => $fh, -cb => $coderef);
Function : prints item data for all docsums. The default printing method is
each item per DocSum is printed with relevant values if present
in a simple table using Text::Wrap.
Returns : none
Args : [optional]
-file : file to print to
-fh : filehandle to print to (cannot be used concurrently with file)
-cb : coderef to use in place of default print method. This is passed
in a DocSum object;
-wrap : number of columns to wrap default text output to (def = 80)
Notes : only applicable for esummary. If -file or -fh are not defined,
prints to STDOUT
Info-related methods
get_available_databases
Title : get_available_databases Usage : my @dbs = $info->get_available_databases Function : returns list of available eutil-compatible database names Returns : Array of strings Args : none Notes : only applicable for einfo.
get_record_count
Title : get_record_count Usage : my $ct = $eutil->get_record_count; Function : returns database record count Returns : integer Args : none Notes : only applicable for einfo.
get_last_update
Title : get_last_update Usage : my $time = $info->get_last_update; Function : returns string containing time/date stamp for last database update Returns : integer Args : none Notes : only applicable for einfo.
get_menu_name
Title : get_menu_name Usage : my $nm = $info->get_menu_name; Function : returns string of database menu name Returns : string Args : none Notes : only applicable for einfo.
get_description
Title : get_description Usage : my $desc = $info->get_description; Function : returns database description Returns : string Args : none Notes : only applicable for einfo.
next_FieldInfo
Title : next_FieldInfo
Usage : while (my $field = $info->next_FieldInfo) {...}
Function : iterate through FieldInfo objects
Returns : Field object
Args : none
Notes : only applicable for einfo. Uses callback() for filtering if defined
for 'fields'
get_FieldInfo
Title : get_FieldInfo Usage : my @fields = $info->get_FieldInfo; Function : returns list of FieldInfo objects Returns : array (FieldInfo objects) Args : none Notes : only applicable for einfo.
next_LinkInfo
Title : next_LinkInfo
Usage : while (my $link = $info->next_LinkInfo) {...}
Function : iterate through LinkInfo objects
Returns : LinkInfo object
Args : none
Notes : only applicable for einfo. Uses callback() for filtering if defined
for 'linkinfo'
get_LinkInfo
Title : get_LinkInfo Usage : my @links = $info->get_LinkInfo; Function : returns list of LinkInfo objects Returns : array (LinkInfo objects) Args : none Notes : only applicable for einfo.
print_FieldInfo
Title : print_FieldInfo
Usage : $info->print_FieldInfo();
$info->print_FieldInfo(-fh => $fh, -cb => $coderef);
Function : prints field data for each FieldInfo object. The default method
prints data from each FieldInfo in a simple table using Text::Wrap.
Returns : none
Args : [optional]
-file : file to print to
-fh : filehandle to print to (cannot be used concurrently with file)
-cb : coderef to use in place of default print method.
-wrap : number of columns to wrap default text output to (def = 80)
Note : if -file or -fh are not defined, prints to STDOUT
print_LinkInfo
Title : print_LinkInfo
Usage : $info->print_LinkInfo();
$info->print_LinkInfo(-fh => $fh, -cb => $coderef);
Function : prints link data for each LinkInfo object. The default is generated
via LinkInfo::to_string
Returns : none
Args : [optional]
-file : file to print to
-fh : filehandle to print to (cannot be used concurrently with file)
-cb : coderef to use in place of default print method. This is passed
in a LinkInfo object;
-wrap : number of columns to wrap default text output to (def = 80)
Notes : only applicable for einfo. If -file or -fh are not defined,
prints to STDOUT
Bio::Tools::EUtilities::Link-related methods
next_LinkSet
Title : next_LinkSet
Usage : while (my $ls = $eutil->next_LinkSet {...}
Function : iterate through LinkSet objects
Returns : LinkSet object
Args : none
Notes : only applicable for elink. Uses callback() for filtering if defined
for 'linksets'
get_LinkSets
Title : get_LinkSets Usage : my @links = $info->get_LinkSets; Function : returns list of LinkSets objects Returns : array (LinkSet objects) Args : none Notes : only applicable for elink.
print_LinkSets
Title : print_LinkSets
Usage : $info->print_LinkSets();
$info->print_LinkSets(-fh => $fh, -cb => $coderef);
Function : prints link data for each LinkSet object. The default is generated
via LinkSet::to_string
Returns : none
Args : [optional]
-file : file to print to
-fh : filehandle to print to (cannot be used concurrently with file)
-cb : coderef to use in place of default print method. This is passed
in a LinkSet object
-wrap : number of columns to wrap default text output to (def = 80)
Notes : only applicable for einfo. If -file or -fh are not defined,
prints to STDOUT
get_linked_databases
Title : get_linked_databases Usage : my @dbs = $eutil->get_linked_databases Function : returns list of databases linked to in linksets Returns : array of databases Args : none Notes : only applicable for elink.
Iterator- and callback-related methods
rewind
Title : rewind
Usage : $esum->rewind()
$esum->rewind('recursive')
Function : retrieve a list of DocSum instances
Returns : array of Bio::Tools::EUtilities::Summary::DocSum
Args : [optional] Scalar; string ('all') to reset all iterators, or string
describing the specific main object iterator to reset. The following
are recognized (case-insensitive):
'all' - rewind all objects and also recursively resets nested object
interators (such as LinkSets and DocSums).
'globalqueries'
'fieldinfo' or 'fieldinfos'
'linkinfo' or 'linkinfos'
'linksets'
'docsums'
generate_iterator
Title : generate_iterator
Usage : my $coderef = $esum->generate_iterator('linkinfo')
Function : generates an iterator (code reference) which iterates through
the relevant object indicated by the args
Returns : code reference
Args : [REQUIRED] Scalar; string describing the specific object to iterate.
The following are currently recognized (case-insensitive):
'globalqueries'
'fieldinfo' or 'fieldinfos'
'linkinfo' or 'linkinfos'
'linksets'
'docsums'
A second argument can also be passed to generate a 'lazy' iterator,
which loops through and returns objects as they are created (instead
of creating all data instances up front, then iterating through,
which is the default). Use of these iterators precludes use of
rewind() for the time being as we can't guarantee you can rewind(),
as this depends on whether the data source is seek()able and thus
'rewindable'. We will add rewind() support at a later time which
will work for 'seekable' data.
A callback specified using callback() will be used to filter objects
for any generated iterator. This behaviour is implemented for both
normal and lazy iterator types and is the default. If you don't want
this, make sure to reset any previously set callbacks via
reset_callback() (which just deletes the code ref).
TODO : generate seekable iterators ala HOP for seekable fh data
callback
Title : callback
Usage : $parser->callback(sub {$_[0]->get_database eq 'protein'});
Function : Get/set callback code ref used to filter returned data objects
Returns : code ref if previously set
Args : single argument:
code ref - evaluates a passed object and returns true or false value
(used in iterators)
'reset' - string, resets the iterator.
returns upon any other args