bp_einfo(1p) [debian man page]
BP_EINFO(1p) User Contributed Perl Documentation BP_EINFO(1p) NAME
einfo.pl - query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases) SYNOPSIS
einfo [-d database] [-f Field Code] [-l Link Name] [-o outfile] DESCRIPTION
Command line options: -e/--email Valid email (required by NCBI policy) -d/--db/--database NCBI database to query (default = none, which shows available databases) -f/--field print out information about a specific field code (default = none) -l/--link print out information about a specific link name (default = none) -o/--out outfile (default = STDOUT) -h/--help show this documentation As per NCBI's policy regarding eutils access, a valid email is required. This is not enforced here (if one is provided you will get a standard warning), but don't be surprised if this doesn't work after June 1, 2010 unless one is supplied. If -d is not specified, field and link arguments are ignored and all available databases are printed instead. If either link names or field codes (or both) are specified, nothing else is printed out (only the info requested). You can specify as many fields and/or links as you want by using multiple -f/-l <ARG> on the command line. AUTHOR - Chris Fields Chris Fields cjfields at bioperl dot org perl v5.14.2 2012-03-02 BP_EINFO(1p)
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Bio::Tools::EUtilities::Info::LinkInfo(3pm) User Contributed Perl Documentation Bio::Tools::EUtilities::Info::LinkInfo(3pm) NAME
Bio::Tools::EUtilities::Info::LinkInfo - class for storing einfo link data SYNOPSIS
## should not create instance directly; Bio::Tools::EUtilities does this ## # get a LinkInfo object using Bio:Tools::EUtilities print "Link name: ",$link->get_link_name," "; print "Link name: ",$link->get_link_menu_name," "; print "Link desc: ",$link->get_link_description," "; print "DBFrom: ",$link->get_dbfrom," "; # database linked from print "DBTo: ",$link->get_dbto," "; # database linked to DESCRIPTION
This class handles data output (XML) from both einfo and elink, and centers on describing data that either describes how NCBI databases are linked together via link names, or how databases are linked to outside databases (LinkOut). Further documentation for Link and Field subclass methods is included below. For more information on einfo see: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html 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. bioperl-l@lists.open-bio.org - 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: 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 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 org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Note : *** should not be called by end-users *** Usage : my $ct = Bio::Tools::EUtilities::Info::LinkInfo; Function : returns new LinkInfo instance Returns : Bio::Tools::EUtilities::Info::LinkInfo instance Args : none (all data added via _add_data, most methods are getters only) get_database Title : get_database Usage : my $db = $info->get_database; Function : returns single database name (eutil-compatible). This is the queried database. For elinks (which have 'db' and 'dbfrom') this is equivalent to db/dbto (use get_dbfrom() to for the latter) Returns : string Args : none get_db (alias for get_database) get_dbto (alias for get_database) get_dbfrom Title : get_dbfrom Usage : my $origdb = $link->get_dbfrom; Function : returns referring database Returns : string Args : none Note : get_link_name Title : get_link_name Usage : $ln = $link->get_link_name; Function : returns raw link name (eutil-compatible) Returns : string Args : none get_link_description Title : get_link_description Usage : $desc = $link->get_link_description; Function : returns the (more detailed) link description Returns : string Args : none get_link_menu_name Title : get_link_menu_name Usage : my $mn = $link->get_link_menu_name; Function : returns formal menu name Returns : string Args : none get_priority Title : get_priority Usage : my $mn = $link->get_priority; Function : returns priority ranking Returns : integer Args : none Note : only set when using elink and cmd set to 'acheck' get_html_tag Title : get_html_tag Usage : my $tag = $link->get_html_tag; Function : returns HTML tag Returns : string Args : none Note : only set when using elink and cmd set to 'acheck' get_url Title : get_url Usage : my $url = $link->get_url; Function : returns URL string; note that the string isn't usable directly but has the ID replaced with the tag <@UID@> Returns : string Args : none Note : only set when using elink and cmd set to 'acheck' 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 : Used generally for debugging and for various print methods perl v5.14.2 2012-03-02 Bio::Tools::EUtilities::Info::LinkInfo(3pm)