Provided by: libbio-eutilities-perl_1.75-4_all bug

NAME

       Bio::Tools::EUtilities - NCBI eutil XML parsers.

VERSION

       version 1.75

SYNOPSIS

         # from file or fh
         my $parser = Bio::Tools::EUtilities->new(
                                              -eutil    => 'einfo',
                                              -file     => 'output.xml'
                                               );

         # or HTTP::Response object...
         my $parser = Bio::Tools::EUtilities->new(
                                              -eutil => 'esearch',
                                              -response => $response
                                               );
         # esearch, esummary, elink
         @ids = $parser->get_ids(); # returns array or array ref of IDs

         # egquery, espell

         $term = $parser->get_term(); # returns array or array ref of IDs

         # elink, einfo

         $db = $parser->get_database(); # returns database

         # Query-related methods (esearch, egquery, espell data)
         # eutil data centered on use of search terms

         my $ct = $parser->get_count; # uses optional database for egquery count
         my $translation = $parser->get_count;

         my $corrected = $parser->get_corrected_query; # espell

         while (my $gquery = $parser->next_GlobalQuery) {
            # iterates through egquery data
         }

         # Info-related methods (einfo data)
         # database-related information

         my $desc = $parser->get_description;
         my $update = $parser->get_last_update;
         my $nm = $parser->get_menu_name;
         my $ct = $parser->get_record_count;

         while (my $field = $parser->next_FieldInfo) {
             # ...
         }
         while (my $field = $parser->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 = $parser->next_History) {
             # ...
         }

         my @hists = $parser->get_Histories;

         # Bio::Tools::EUtilities::Summary (esummary data)
         # information on a specific database record

         # retrieve nested docsum data
         while (my $docsum = $parser->next_DocSum) {
             print "ID:",$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 = $parser->next_DocSum) {
            my @items = $docsum->get_all_DocSum_Items;
         }

DESCRIPTION

       Parses NCBI eutils XML output for retrieving IDs and other information. Part of the
       BioPerl EUtilities system.

       This is a general parser for eutils XML; data from efetch is NOT parsed (this requires
       separate format-dependent parsers). All other XML for eutils is parsed.  These modules can
       be used independently of Bio::DB::EUtilities and Bio::Tools::EUtilities::EUtilParameters;
       if used in this way, only data present in the XML will be parsed out (other bits are
       retrieved from a passed-in Bio::Tools::EUtilities::EUtilParameters instance used while
       querying the database)

TODO

       This module is largely complete. However there are a few holes which will eventually be
       filled in. TranslationSets from esearch are not currently parsed, for instance.

   Constructor methods
   new
        Title    : new
        Usage    : my $parser = Bio::Tools::EUtilities->new(-file => 'my.xml',
                                                           -eutil => 'esearch');
        Function : create Bio::Tools::EUtilities instance
        Returns  : new Bio::Tools::EUtilities instance
        Args     : -file/-fh - File or filehandle
                   -eutil    - eutil parser to use (supports all but efetch)
                   -response - HTTP::Response object (optional)

Bio::Tools::EUtilities methods

   cache_response
        Title    : cache_response
        Usage    : $parser->cache_response(1)
        Function : sets flag to cache response object (off by default)
        Returns  : value eval'ing to TRUE or FALSE
        Args     : value eval'ing to TRUE or FALSE
        Note     : must be set prior to any parsing run

   response
        Title    : response
        Usage    : my $response = $parser->response;
        Function : Get/Set HTTP::Response object
        Returns  : HTTP::Response
        Args     : HTTP::Response
        Note     : to prevent object from destruction set cache_response() to TRUE

   parameter_base
        Title    : parameter_base
        Usage    : my $response = $parser->parameter_base;
        Function : Get/Set Bio::ParameterBaseI object (should be Bio::Tools::EUtilities::EUtilParameters)
        Returns  : Bio::Tools::EUtilities::EUtilParameters || undef
        Args     : (optional) Bio::Tools::EUtilities::EUtilParameters
        Note     : If this object is present, it may be used as a last resort for
                   some data values if parsed XML does not contain said values (for
                   instance, database, term, IDs, etc).

   data_parsed
        Title    : data_parsed
        Usage    : if ($parser->data_parsed) {...}
        Function : returns TRUE if data has been parsed
        Returns  : value eval'ing to TRUE or FALSE
        Args     : none (set within parser)
        Note     : mainly internal method (set in case user wants to check
                   whether parser is exhausted).

   is_lazy
        Title    : is_lazy
        Usage    : if ($parser->is_lazy) {...}
        Function : returns TRUE if parser is set to lazy parsing mode
                   (only affects elink/esummary)
        Returns  : Boolean
        Args     : none
        Note     : Permanently set in constructor.  Still highly experimental.
                   Don't stare directly at happy fun ball...

   parse_data
        Title    : parse_data
        Usage    : $parser->parse_data
        Function : direct call to parse data; normally implicitly called
        Returns  : none
        Args     : none

   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 the parser 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::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

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 db/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
                   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, or the available databases
                   espell     : the queried database
                   elink      : collected from each LinkSet
                   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 (History 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, -callback => $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 data is generated
                   via DocSum::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 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 link data for each FieldInfo object. The default is generated
                   via FieldInfo::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 FieldInfo 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

   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.  Now defers to get_databases.

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' - GlobalQuery objects
                   'fieldinfo' or 'fieldinfos' - FieldInfo objects
                   'linkinfo' or 'linkinfos' - LinkInfo objects in this layer
                   'linksets' - LinkSet objects
                   'docsums' - DocSum objects
                   'histories' - HistoryI objects (Cookies, LinkSets)

   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' (the latter sounds clumsy, but I alias it JIC)
                   'linkinfo' or 'linkinfos' (the latter sounds clumsy, but I alias it JIC)
                   'linksets'
                   'docsums'
                   'histories'

        Note     : This function generates a simple coderef that one can use
                   independently of the various next_* functions (in fact, the next_*
                   functions use lazily created iterators generated via this method,
                   while rewind() merely deletes them so they can be regenerated on the
                   next call).

                   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).  Note that setting
                   callback() also changes the behavior of the next_* functions as the
                   iterators are generated here (as described above); this is a feature
                   and not a bug.

                   'Lazy' iterators are considered an experimental feature and may be
                   modified in the future. A 'lazy' iterator, which loops through and
                   returns objects as they are created (instead of creating all data
                   instances up front, then iterating through) is returned if the
                   parser is set to 'lazy' mode. This mode is only present for elink
                   and esummary output as they are the two formats parsed which can
                   generate potentially thousands of individual objects (note efetch
                   isn't parsed, so isn't counted). Use of rewind() with these
                   iterators is not supported 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 or possibly cached
                   objects via Storable or BDB.

   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

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/%%7Bdist%7D

AUTHOR

       Chris Fields <cjfields@bioperl.org>

COPYRIGHT

       This software is copyright (c) 2006-2013 by Chris Fields.

       This software is available under the same terms as the perl 5 programming language system
       itself.