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::FieldInfo(3pm) User Contributed Perl Documentation Bio::Tools::EUtilities::Info::FieldInfo(3pm) NAME
Bio::Tools::EUtilities::Info::FieldInfo - class for storing einfo field data SYNOPSIS
#### should not create instance directly; Bio::Tools::EUtilities does this #### my $info = Bio::Tools::EUtilities->new(-eutil => 'einfo', -file => 'einfo.xml'); # can also use '-response' (for HTTP::Response objects) or '-fh' (for filehandles) # print available databases (if data is present) print join(', ',$info->get_available_databases)," "; # get database info my $db = $info->get_database; # in case you forgot... my $desc = $info->get_description; my $nm = $info->get_menu_name; my $ct = $info->get_record_count; my $dt = $info->get_last_update; # EUtilDataI interface methods my $eutil = $info->eutil; my $type = $info->type; # iterate through Field and Link objects while (my $field = $info->next_Field) { print "Field code: ",$field->get_field_code," "; print "Field name: ",$field->get_field_name," "; print "Field desc: ",$field->get_field_description," "; print "DB : ",$field->get_database," "; print "Term ct : ",$field->get_term_count," "; for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) { print " Field $att " if $field->$att; } } my @fields = $info->get_Fields; # grab them all (useful for grep) $info->rewind('fields'); # rewinds Field iterator DESCRIPTION
This class handles simple field data output (XML) from einfo. 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::FieldInfo; Function : returns new FieldInfo instance Returns : Bio::Tools::EUtilities::Info::FieldInfo instance Args : none (all data added via _add_data, most methods are getters only) get_term_count Title : get_term_count Usage : my $ct = $field->get_term_count; Function : returns number of terms for field Returns : integer Args : none get_field_name Title : get_field_name Usage : my $nm = $field->get_field_name; Function : returns the full name of the field Returns : string Args : none get_full_name Title : get_full_name Note : alias of get_field_name() get_field_code Title : get_field_code Usage : $field->get_field_code() Function : returns field code (abbreviation) used for queries Returns : string Args : none get_field_description Title : get_field_description Usage : $field->get_field_description Function : returns field description Returns : string Args : none Note : alias of get_description() is_date Title : is_date Usage : if ($field->is_date) {...} Function : returns true if field contains date information Returns : Boolean Args : none is_singletoken Title : is_singletoken Usage : if ($field->is_singletoken) {...} Function : returns true if field has single value in docsums Returns : Boolean Args : none is_hierarchy Title : is_hierarchy Usage : if ($field->is_hierarchy) {...} Function : returns true if field contains hierarchal values Returns : Boolean Args : none is_hidden Title : is_hidden Usage : if ($field->is_hidden) {...} Function : returns true if field is hidden in docsums Returns : Boolean Args : none is_numerical Title : is_numerical Usage : if ($field->is_numerical) {...} Function : returns true if field contains a numerical value Returns : Boolean 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 : Used generally for debugging and for various print methods perl v5.14.2 2012-03-02 Bio::Tools::EUtilities::Info::FieldInfo(3pm)