NAME

Bio::MAGETAB::Util::Reader - A parser/validator for MAGE-TAB documents.

SYNOPSIS

use Bio::MAGETAB::Util::Reader;
my $reader = Bio::MAGETAB::Util::Reader->new({
   idf            => $idf,
   relaxed_parser => $is_relaxed,
});

my $magetab = $reader->parse();

DESCRIPTION

This is the main parsing and validation class which can be used to read a MAGE-TAB document into a set of Bio::MAGETAB classes for further manipulation.

ATTRIBUTES

idf

A filesystem or URI path to the top-level IDF file describing the investigation. This attribute is *required*.

relaxed_parser

A boolean value (default FALSE) indicating whether or not the parse should take place in "relaxed mode" or not. The regular parsing mode will throw an exception in cases where an object is referenced before it has been declared (e.g., Protocol REF pointing to a non-existent Protocol Name). Relaxed parsing mode will silently autogenerate the non-existent objects instead.

namespace

An optional namespace string to be used in object creation.

authority

An optional authority string to be used in object creation.

builder

An optional Builder object. These Builder objects are used to track the creation of Bio::MAGETAB objects by caching the objects in an internal store, keyed by a set of identifying information (see the Builder class). This object can be used in multiple Reader objects to help link common objects from multiple MAGE-TAB documents together. In its simplest form this internal store is a simple hash; however in principle this could be extended by subclassing Builder to create e.g. persistent database storage mechanisms.

ignore_datafiles

A boolean value (default FALSE) indicating whether to skip parsing of Data Matrix files.

common_directory

A boolean value (default TRUE) indicating whether the IDF, SDRF, ADF and Data Matrices are located in the same directory. This influences whether URIs found in IDF and SDRF files are interpreted relative to the locations of those files, or relative to the current working directory. Note that this will not affect local file URIs giving absolute locations or URIs using other schemes (e.g. http).

document_version

A string representing the MAGE-TAB version used in the parsed document. This is populated by the parse() method.

METHODS

parse

Attempts to parse the full MAGE-TAB document, starting with the top-level IDF file, and returns the resulting Bio::MAGETAB container object in scalar context, or the top-level Bio::MAGETAB::Investigation object and container object in list context.

SEE ALSO

Bio::MAGETAB

AUTHOR

Tim F. Rayner <tfrayner@gmail.com>

LICENSE

This library is released under version 2 of the GNU General Public License (GPL).