/ 
Bio-EUtilities-1.74
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/ Bio::Tools::EUtilities

NAME

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

VERSION

version 1.74

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
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.

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
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
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.
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
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.
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.