Provided by: libboulder-perl_1.30-6_all 
NAME
Boulder - An API for hierarchical tag/value structures
SYNOPSIS
# Read a series of People records from STDIN.
# Add an "Eligibility" attribute to all those whose
# Age >= 35 and Friends list includes "Fred"
use Boulder::Stream;
my $stream = Boulder::Stream->newFh;
while ( my $record = <$stream> ) {
next unless $record->Age >= 35;
my @friends = $record->Friends;
next unless grep {$_ eq 'Fred'} @friends;
$record->insert(Eligibility => 'yes');
print $stream $record;
}
Related manual pages:
basics
------
Stone hierarchical tag/value records
Stone::Cursor Traverse a hierarchy
Boulder::Stream stream-oriented storage for Stones
Boulder::Store record-oriented storage for Stones
Boulder::XML XML conversion for Stones
Boulder::String conversion to strings
genome-related
---------------
Boulder::Genbank parse Genbank (DNA sequence) records
Boulder::Blast parse BLAST (basic local alignment search tool) reports
Boulder::Medline parse Medline (pubmed) records
Boulder::Omim parse OMIM (online Mendelian inheritance in man) records
Boulder::Swissprot parse Swissprot records
Boulder::Unigene parse Unigene records
DESCRIPTION
Boulder IO
Boulder IO is a simple TAG=VALUE data format designed for sharing data between programs
connected via a pipe. It is also simple enough to use as a common data exchange format
between databases, Web pages, and other data representations.
The basic data format is very simple. It consists of a series of TAG=VALUE pairs
separated by newlines. It is record-oriented. The end of a record is indicated by an
empty delimiter alone on a line. The delimiter is "=" by default, but can be adjusted by
the user.
An example boulder stream looks like this:
Name=Lincoln Stein
Home=/u/bush202/lds32
Organization=Cold Spring Harbor Laboratory
Login=lds32
Password_age=20
Password_expires=60
Alias=lstein
Alias=steinl
=
Name=Leigh Deacon
Home=/u/bush202/tanager
Organization=Cold Spring Harbor Laboratory
Login=tanager
Password_age=2
Password_expires=60
=
Notes:
(1) There is no need for all tags to appear in all records, or indeed for all the records
to be homogeneous.
(2) Multiple values are allowed, as with the Alias tag in the second record.
(3) Lines can be any length, as in a potential 40 Kbp DNA sequence entry.
(4) Tags can be any alphanumeric character (upper or lower case) and may contain embedded
spaces. Conventionally we use the characters A-Z0-9_, because they can be used
without single quoting as keys in Perl associative arrays, but this is merely
stylistic. Values can be any character at all except for the reserved characters {}=%
and newline. You can incorporate binary data into the data stream by escaping these
characters in the URL manner, using a % sign followed by the (capitalized) hexadecimal
code for the character. The module makes this automatic.
Hierarchical Records
The simple boulder format can be extended to accommodate nested relations and other
intresting structures. Nested records can be created in this way:
Name=Lincoln Stein
Home=/u/bush202/lds32
Organization=Cold Spring Harbor Laboratory
Login=lds32
Password_age=20
Password_expires=60
Privileges={
ChangePasswd=yes
CronJobs=yes
Reboot=yes
Shutdown=no
}
=
Name=Leigh Deacon
Home=/u/bush202/tanager
Organization=Cold Spring Harbor Laboratory
Login=tanager
Password_age=2
Password_expires=60
Privileges={
ChangePasswd=yes
CronJobs=no
Reboot=no
Shutdown=no
}
=
As in the original format, tags may be multivalued. For example, there might be several
Privilege record assigned to a login account. Each subrecord may contain further
subrecords.
Within the program, a hierarchical record is encapsulated within a "Stone", an opaque
structure that implements methods for fetching and settings its various tags.
Using Boulder for I/O
The Boulder API was designed to make reading and writing of complex hierarchical records
almost as easy as reading and writing single lines of text.
Boulder::Stream
The main component of the Boulder modules is Boulder::Stream, which provides a stream-
oriented view of the data. You can read and write to Boulder::Streams via tied
filehandles, or via method calls. Data records are flattened into a simple format
called "boulderio" format.
Boulder::XML
Boulder::XML acts like Boulder::Stream, but the serialization format is XML. You need
XML::Parser installed to use this module.
Boulder::Store
This is a simple persistent storage class which allows you to store several (thousand)
Stone's into a DB_File database. You must have libdb and the Perl DB_File extensions
installed in order to take advantage of this class.
Boulder::Genbank
Boulder::Unigene
Boulder::OMIM
Boulder::Blast
Boulder::Medline
Boulder::SwissProt
These are parsers and accessors for various biological data sources. They act like
Boulder::Stream, but return a set of Stone objects that have certain prescribed tags
and values. Many of these modules were written by Luca I.G. Toldo
<luca.toldo@merck.de>.
Stone Objects
The Stone object encapsulates a set of tags and values. Any tag can be single- or
multivalued, and tags are allowed to contain subtags to any depth. A simple set of
methods named tags(), get(), put(), insert(), replace() and so forth, allows you to
examine the tags that are available, get and set their values, and search for particular
tags. In addition, an autoload mechanism allows you to use method calls to access tags,
for example:
my @friends = $record->Friends;
is equivalent to:
my @friends = $record->get('Friends');
A Stone::Cursor class allows you to traverse Stones systematically.
A full explanation of the Stone class can be found in its manual page.
AUTHOR
Lincoln D. Stein <lstein@cshl.org>, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
This module can be used and distributed on the same terms as Perl itself.
SEE ALSO
Boulder::Blast, Boulder::Genbank, Boulder::Medline, Boulder::Unigene, Boulder::Omim,
Boulder::SwissProt