Bio::DB::EUtilities::esummary - retrieval of NCBI DocSum data from a list of primary IDs or a Cookie
Do not use this module directly. Use it via the Bio::DB::EUtilities class.
use Bio::DB::EUtilities; my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'pubmed', -term => 'hutP', -usehistory => 'y'); $esearch->get_response; # parse the response, fetch a cookie my $esummary = Bio::DB::EUtilities->new(-eutil => 'esummary', -cookie => $esearch->next_cookie); print $esearch->get_response-content; # prints XML output
WARNING: Please do NOT spam the Entrez web server with multiple requests.
The EUtility ESummary is used to retrieve ducument summaries from a list of primary IDs or the user's history (stored on the remote server and accessible using a Cookie. The returned data is processed for errors, but no further processing is done at this time.
db
one or more database available through EUtilities if set to 'all', will retrieve all related ID's from each database (see method get_db_ids to retrieve these)
id
a list of primary ID's (see below)
reldate
limits results to the number of days preceding today's date
mindate
maxdate
limits results by dates (yyyy/mm/dd format, or by year)
yyyy/mm/dd
term
limits results by Entrez query (only valid when cmd=neighbor within a single database)
cmd=neighbor
retmode
set to XML, but can be changed to ref when needed
cookie
a Bio::DB::EUtilities::Cookie object (see below)
cmd
command values (see below)
holding
list LinkOut URLs for specified holding provider; used with cmd=llinks or cmd=llinkslib (rarely used)
cmd=llinks
cmd=llinkslib
Command values are set using the cmd parameter.
prlinks
List the hyperlink to the primary LinkOut provider for multiple IDs and database. Each ID is processed separately.
prlinks&retmode=ref
Create a hyperlink to the primary LinkOut provider for a single ID and database.
llinks
List LinkOut URLs and Attributes, except PubMed libraries, for multiple IDs and database. Each ID is processed separately.
llinkslib
List LinkOut URLs and Attributes for multiple IDs and database. Each ID is processed separately.
lcheck
Check for the existence (Y or N) of an external link in for multiple IDs and database.
ncheck
Check for the existence of a neighbor link for each ID within a database, e.g., Related Articles in PubMed.
neighbor
The default setting. Display neighbors and their scores within a database.
neighbor_history
Create history (WebEnv & query_key) for use in other EUtilities.
acheck
Lists Entrez databases links for multiple IDs from a single database.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@lists.open-bio.org - General discussion http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
http://bugzilla.open-bio.org/
Email cjfields at uiuc dot edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : parse_response Usage : $db->parse_response($content) Function: parse out response for cookie and/or id's Returns : none Args : HTTP::Response object Throws : 'NCBI elink nonrecoverable error'
Title : cookie Usage : $db->add_cookie($cookie) Function: adds an NCBI query cookie to the internal cookie queue Returns : none Args : a Bio::DB::EUtilities::Cookie object
Title : next_cookie Usage : $cookie = $db->next_cookie Function: return a cookie from the internal cookie queue Returns : a Bio::DB::EUtilities::Cookie object Args : none
Title : reset_cookie Usage : $db->reset_cookie Function: resets the internal cookie queue Returns : none Args : none
Title : get_all_cookies Usage : @cookies = $db->get_all_cookies Function: retrieves all cookies from the internal cookie queue; this leaves the cookies in the queue intact Returns : none Args : none
Title : get_response Usage : $db->get_response($content) Function: main method to retrieve data stream; parses out response for cookie Returns : HTTP::Response object Args : optional : Bio::DB::EUtilities::Cookie from a previous search Throws : 'not a cookie' exception, response errors (via HTTP::Response)
Title : reset_parameters Usage : $db->reset_parameters(@args); Function: resets the parameters for a EUtility with args (in @args) Returns : none Args : array of arguments (arg1 => value, arg2 => value)
Experimental method at this time
Title : count Usage : $count = $db->count; Function: return count of number of entries retrieved by query Returns : integer Args : none
Title : get_db_ids Usage : $count = $elink->get_db_ids($db); # gets array ref of IDs @count = $elink->get_db_ids($db); # gets array of IDs %hash = $elink->get_db_ids(); # hash of databases (keys) and array_refs(value) Function: returns an array or array ref if a database is the argument, otherwise returns a hash of the database (keys) and id_refs (values) Returns : array or array ref of ids (arg=database) or hash of database-array_refs (no args) Args : database string;
Title : get_score Usage : $score = $db->get_score($id); Function: gets score for ID (if present) Returns : integer (score) Args : ID values
Title : get_ids_by_score Usage : @ids = $db->get_ids_by_score; # returns IDs @ids = $db->get_ids_by_score($score); # get IDs by score Function: returns ref of array of ids based on relevancy score from elink; To return all ID's above a score, use the normal score value; to return all ID's below a score, append the score with '-'; Returns : ref of array of ID's; if array, an array of IDs Args : integer (score value); returns all if no arg provided
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.