Bio::Tools::EUtilities::Info::FieldInfo - class for storing einfo field data
#### 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),"\n"; # 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,"\n"; print "Field name: ",$field->get_field_name,"\n"; print "Field desc: ",$field->get_field_description,"\n"; print "DB : ",$field->get_database,"\n"; print "Term ct : ",$field->get_term_count,"\n"; for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) { print "\tField $att\n" if $field->$att; } } my @fields = $info->get_Fields; # grab them all (useful for grep) while (my $link = $info->next_Link) { print "Link name: ",$link->get_link_name,"\n"; print "Link desc: ",$link->get_link_description,"\n"; print "DBFrom: ",$link->get_dbfrom,"\n"; # same as get_database() print "DBTo: ",$link->get_dbto,"\n"; # database linked to } my @links = $info->get_Links; # grab them all (useful for grep) $info->rewind(); # rewinds all iterators $info->rewind('links'); # rewinds Link iterator $info->rewind('fields'); # rewinds Field iterator
This class handles data output (XML) from einfo.
einfo is capable of returning two types of information: 1) a list of all available databases (when called w/o parameters) and 2) information about a specific database. The latter information includes the database description, record count, and date/time stamp for the last update, among other things. It also includes a list of fields (indices by which record data is stored which can be used in queries) and links (crossrefs between related records in other databases at NCBI). Data from the latter two are stored in two small subclasses (Field and Link) which can be iterated through or retrieved all at once, as demonstrated above. NOTE: Methods described for the Link and Field subclasses are unique to those classes (as they retrieve data unique to those data types).
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
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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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
Title : term_count Usage : my $ct = $field->term_count; Function : returns number of terms for field Returns : integer Args : none
Title : get_field_name Usage : my $nm = $field->get_field_name; Function : returns the full name of the field Returns : string Args : none
Title : get_full_name Note : alias of get_field_name()
Title : get_field_code Usage : $field->get_field_code() Function : returns field code (abbreviation) used for queries Returns : string Args : none
Title : get_field_description Usage : $field->get_field_description Function : returns field description Returns : string Args : none Note : alias of get_description()
Title : is_date Usage : if ($field->is_date) {...} Function : returns true if field contains date information Returns : Boolean Args : none
Title : is_singletoken Usage : if ($field->is_singletoken) {...} Function : returns true if field has single value in docsums Returns : Boolean Args : none
Title : is_hierarchy Usage : if ($field->is_hierarchy) {...} Function : returns true if field contains hierarchal values Returns : Boolean Args : none
Title : is_hidden Usage : if ($field->is_hidden) {...} Function : returns true if field is hidden in docsums Returns : Boolean Args : none
Title : is_numerical Usage : if ($field->is_numerical) {...} Function : returns true if field contains a numerical value Returns : Boolean Args : none
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
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.