Bio::D...ilities(3pm)

💖 NAME 💖

okay bestie, welcome to the Bio::DB::EUtilities page (that's the 3pm one, Perl gang rise up 🫶). It's a webagent that talks to and pulls data from NCBI's eUtils. That's the whole vibe. Slay.

---

✨ VERSION ✨

version 1.77 💅

---

🌈 SYNOPSIS 🌈

my $eutil = Bio::DB::EUtilities->new(
  -eutil      => 'esearch',
  -term       => 'BRCA1',
  -db         => 'pubmed',
  -retmax     => 10000,
  -email      => 'foo@bar.org'); # 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 💜

okay so here's the tea: this is a general webagent that posts and retrieves data to NCBI's eUtils service using their CGI interface. ✨ A separate project — currently chillin' in BioPerl-Run — uses the SOAP-based interface for eUtils instead. Two paths, same destiny.

fr fr, a full explanation of the eUtils interfaces is not possible within this short module, bestie. The module is small, the interface is huge, that's just the way it is 😭. For more details, go look at the BioPerl wiki HOWTO. 👑

---

🔥 METHODS 🔥

📝 TODO 📝

the to-do list, no cap:

• Finish documentation — the HOWTOs, both standard and Cookbook. 📚
• Cookbook tests — set up dev-only tests for Cookbook examples so they stay consistently updated. (iconic idea, honestly.)
• API — Mark Jensen has written up the SOAP-based eUtil modules, and maybe we should coalesce around a consistent API between the two (they are close). lowkey a glow-up waiting to happen.
• 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?
• Moosify? — not necessary, but it might make things easier and more maintainable in the long run. 💅

---

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

🚨 heads up bestie: -file and -cb are not a duo. can't use file and callback at the same time. pick one, queen.

🫶 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. so like, delay_policy() is the main character here and delay is the override button. iykyk.

---

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.

🧚 NCBI said 3 requests per second, periodt. this method implements that policy. and yes, it will likely change to check time of day or number of requests for lengthening delays — so don't get too attached to the exact behavior, it's giving "future glow-up".

🦋 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

🌸 reminder: this one is an abstract method — it's defined by the implementation, not here. the subclasses carry it, bestie.

---

Bio::Tools::EUtilities::EUtilParameters-delegating methods

okay so this is only a subset of the parameters available from Bio::Tools::EUtilities::EUtilParameters — specifically the ones deemed absolutely necessary. All the others? You get them by calling 'parameter_base->method' whenever you need them. 💅

⭐ 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)

👀 note the tea: this sets any parameter — it does not screen them. so be careful, it'll just take whatever you hand it.

⭐ 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

(to be continued, bestie — this page is long and we're just getting started 💖)

🦋 Bio::Tools::EUtilities::EUtilDataI methods 🦋

💅 eutil

• Title: eutil
• Usage: $eutil->$foo->eutil
• Function: get it / set it — the eutil
• Returns: string
• Args: string (eutil)
• Throws: on invalid eutil

💅 datatype

• Title: datatype
• Usage: $type = $foo->datatype;
• Function: get it / set it — the data object type
• Returns: string
• Args: string

💅 to_string

• Title: to_string
• Usage: $foo->to_string()
• Function: converts the current object to a 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 the data in the parser. Unless you hand it a coderef, 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 the 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, it prints to STDOUT

---

🫶 Methods useful for multiple eutils 🫶

⭐ get_ids

• Title: get_ids
• Usage: my @ids = $parser->get_ids
• Function: returns an array of the requested IDs (peep the Notes for the specifics)
• Returns: array
• Args: [conditional] not required except when running elink queries against multiple databases. In that case the database name is optional but recommended when retrieving IDs, since the ID list will be globbed together. If a db name isn't provided in those situations, a warning is issued as a lil 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 a 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's 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 a 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 the 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) are stored on the remote server. Access to this data is wrapped up in a 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 lets you 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 a 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 the count from a 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: the 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: the 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 an 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 a 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 gets printed with the 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 the 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, it 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 gets printed with the 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 the 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, it prints to STDOUT

Info-related methods 💖

okay bestie, this next batch is all about pulling info out of your eutils. let's go! ✨

get_available_databases ✨

• Title: get_available_databases
• Usage:

my @dbs = $info->get_available_databases

• Function: hands you back a list of eutil-compatible database names, no cap.
• Returns: an 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: gives you the database record count.
• Returns: an integer.
• Args: none.
• Notes: only applicable for einfo.

get_last_update ⏰

• Title: get_last_update
• Usage: my $time = $info->get_last_update;
• Function: returns a string containing the time/date stamp for the last database update.
• Returns: an integer. (Yes, it says integer, bestie. That's what the page says.)
• Args: none.
• Notes: only applicable for einfo.

get_menu_name 📋

• Title: get_menu_name
• Usage: my $nm = $info->get_menu_name;
• Function: returns a string of the database menu name.
• Returns: a string.
• Args: none.
• Notes: only applicable for einfo.

get_description 📝

• Title: get_description
• Usage: my $desc = $info->get_description;
• Function: returns the database description.
• Returns: a 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: a 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 a list of FieldInfo objects.
• Returns: an array of 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: a 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 a list of LinkInfo objects.
• Returns: an array of 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 🔗

links links links, bestie! let's get into the link sets and linked databases. 🦋

next_LinkSet 🔁

• Title: next_LinkSet
• Usage: while (my $ls = $eutil->next_LinkSet {...}
• Function: iterate through LinkSet objects.
• Returns: a 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 a list of LinkSets objects.
• Returns: an array of 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 a list of databases linked to in linksets.
• Returns: an array of databases.
• Args: none.
• Notes: only applicable for elink.

---

Iterator- and callback-related methods 🎀

iterators and callbacks, the way that these let you loop through your data? iconic. 💅

rewind ⏪

• Title: rewind
• Usage:

$esum->rewind()
$esum->rewind('recursive')

• Function: retrieve a list of DocSum instances.
• Returns: an 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 iterators (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: a 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: a 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

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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
• https://bioperl.org/Support.html — 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 responsive 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/bio-eutilities/issues

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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.

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✨ That's the whole vibe, bestie! This page was brought to you by perl v5.40.0, dated 2025-01-27, and it's the manual for Bio::D...ilities(3pm). Now go slay those eutils! 💅