Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::MAGETAB::Util::ReUser(Contributed Perl DocumBio::MAGETAB::Util::Reader(3)

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).

perl v5.32.1			  2013-04-30	 Bio::MAGETAB::Util::Reader(3)

NAME | SYNOPSIS | DESCRIPTION | ATTRIBUTES | METHODS | SEE ALSO | AUTHOR | LICENSE

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::MAGETAB::Util::Reader&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help