Bio::Tools::EUtilities::Summary::Item - simple layered object for DocSum item data
# Items can be nested up to three levels at this time. These levels can be # accessed via Item, ListItem, or StructureItem methods: while (my $item = $docsum->next_Item) { print "Name: ",$item->get_name,"\n"; print "Data: ",$item->get_content,"\n"; print "Type: ",$item->get_type,"\n"; while (my $ls = $item->next_ListItem) { # do same here while (my $struct = $ls->next_StructureItem) { # do more stuff here } } }
DocSum data, as returned from esummary, normally is a simple list of item-content-content_type groups. However, items can also contain nested data to represent more complex data (such as structural data). Up to three nested layers may appear in any document summary.
This class contains methods to access data that can appear in a docsum for any individual item as well as describes methods to traverse the hierarchy of items present in a document summary.
The unique name for items are accessed via get_name(), the content by get_content() (if present), and the data type by get_type(). Items can have ListItems (Item objects with a datatype() 'list'), which in turn can have StructureItems (Item objects with a datatype of 'structure'). Items are initially traversed via a DocSum object using next_Item() or obtained all at once with get_Items(). Similarly, nested Items can be accessed by using next_ListItem/get_ListItems and next_StructureItem/get_StructureItem. A flattened list of items can be accessed with get_all_Items().
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Function : Returns : Args :
Title : get_ids Usage : my ($id) = $item->get_ids; Function : returns array or array ref with id Returns : array or array ref Args : none Note : the behavior of this method is to remain consistent with other implementations of get_ids(). To retrieve the single DocSum ID use get_id()
Title : get_id Usage : my ($id) = $item->get_id; Function : returns UID of record Returns : integer Args : none
Title : next_ListItem Usage : while (my $ls = $item->next_ListItem) {...} Function : iterates through ListItems (nested layer of Item) Returns : single ListItem Args : none
Title : get_ListItems Usage : my @ls = $item->get_ListItems Function : returns list of, well, List Items Returns : array of List Items Args : none
Title : next_StructureItem Usage : while (my $struc = $ls->next_StructureItem) {...} Function : iterates through StructureItems (nested layer of ListItem) Returns : single StructureItems Args : none
Title : get_StructureItems Usage : my @structs = $ls->get_StructureItems Function : returns list of Structure Items Returns : array of StructureItems Args : none
Title : next_subItem Usage : while (my $it = $ls->next_subItem) {...} Function : iterates through the next layer of Items Returns : single Item Args : none Notes : unlike next_ListItem and next_StructureItem, this generically accesses any sub Items (useful for recursive calls, for example)
Title : get_subItems Usage : my @items = $ls->get_subItems Function : returns list of sub Items Returns : array of Items Args : none Notes : unlike get_ListItems and get_StructureItems, this generically accesses any sub Items (useful for recursive calls, for example)
Title : get_name Usage : my $nm = $ls->get_name Function : retrieves Item/ListItem/StructureItem name for this Item Returns : string Args : none
Title : get_type Usage : my $type = $ls->get_type Function : retrieves Item/ListItem/StructureItem type Returns : string Args : none Note : this is not the same as the datatype(), which describes the group this Item object belongs to
Title : get_content Usage : my $data = $ls->get_content Function : retrieves Item/ListItem/StructureItem content (if any) Returns : string Args : none
Title : rewind Usage : $item->rewind() Function : rewinds iterators Returns : none Args : [optional] No arg - only rewinds current layer 'all' - rewind all DocSum object layers (Items, ListItems, StructureItems)
Title : next_Item Usage : while (my $item = $docsum->next_Item) {...} Function : iterates through Items (nested layer of Item) Returns : single Item Args : [optional] single arg (string) 'flatten' - iterates through a flattened list ala get_all_DocSum_Items()
Title : get_Items Usage : my @items = $docsum->get_Items Function : returns list of, well, Items Returns : array of Items Args : none
Title : get_all_Items Usage : my @items = $docsum->get_all_Items Function : returns flattened list of all Item objects (Items, ListItems, StructureItems) Returns : array of Items Args : none Note : items are added top-down (similar order to using nested calls) in original list order. 1 2 7 8 Item - Item - Item - Item ... | | 3 6 ListItem - ListItem | | 4 5 Structure - Structure
Title : get_all_names Usage : my @names = get_all_names() Function : Returns an array of names for all Item(s) in DocSum. Returns : array of unique strings Args : none
Title : get_Items_by_name Usage : my @items = get_Items_by_name('CreateDate') Function : Returns named Item(s) in DocSum (indicated by passed argument) Returns : array of Item objects Args : string (Item name)
Title : get_contents_by_name Usage : my ($data) = get_contents_by_name('CreateDate') Function : Returns content for named Item(s) in DocSum (indicated by passed argument) Returns : array of values (type varies per Item) Args : string (Item name)
Title : get_type_by_name Usage : my $data = get_type_by_name('CreateDate') Function : Returns data type for named Item in DocSum (indicated by passed argument) Returns : scalar value (string) if present Args : string (Item name)
Title : to_string Usage : $foo->to_string() Function : converts current object to string Returns : none Args : (optional) simple data for text formatting. This implementation passes an argument for layering Items/subItems Note : Used generically for debugging and print_DocSums 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.