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Bio::Assembly::IO(3)  User Contributed Perl Documentation Bio::Assembly::IO(3)

NAME
       Bio::Assembly::IO - Handler for Assembly::IO Formats

SYNOPSIS
	   use Bio::Assembly::IO;

	   $in	= Bio::Assembly::IO->new(-file=>"<inputfilename",
					 -format=>'phrap');
	   $out = Bio::Assembly::IO->new(-file=>">outputfilename",
					 -format=>'phrap');

	   while ( my $scaffold = $in->next_assembly() ) {
	      # do something with Bio::Assembly::Scaffold instance
	      # ...
	      $out->write_assembly(-scaffold => $scaffold);
	   }

	   $in->close;
	   $out->close;

DESCRIPTION
       Bio::Assembly::IO is a handler module for formats in the Assembly::IO
       set (e.g. Bio::Assembly::IO::phrap).

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing lists  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track
       the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR
       Robson Francisco de Souza

       E-mail: rfsouza@citri.iq.usp.br

CONTRIBUTORS
       #

APPENDIX
       The rest of the documentation details each of the object methods.
       Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: Bio::Assembly::IO->new(-file =>$filename,-format=>'format')
	Function: Returns a new assembly stream
	Returns : A Bio::Assembly::IO::Handler initialised
		  with the appropriate format
	Args	: -file => $filename
		  -format => format

   next_assembly
	Title	: next_assembly
	Usage	: $cluster = $stream->next_assembly()
	Function: Reads the next assembly object from the stream and returns it.
	Returns : a Bio::Assembly::ScaffoldI compliant object
	Args	: none

   write_assembly
	 Title	 : write_assembly
	 Usage	 : $ass_io->write_assembly($assembly)
	 Function: Write the assembly object in Phrap compatible ACE format
	 Returns : 1 on success, 0 for error
	 Args	 : A Bio::Assembly::Scaffold object

   _load_format_module
	Title	: _load_format_module
	Usage	: *INTERNAL Assembly::IO stuff*
	Function: Loads up (like use) a module at run time on demand
	Example :
	Returns :
	Args	:

   _guess_format
	Title	: _guess_format
	Usage	: $obj->_guess_format($filename)
	Function: guess format based on file suffix
	Example :
	Returns : guessed format of filename (lower case)
	Args	:
	Notes	: formats that _filehandle() will guess includes
		  only phrap, by now.

perl v5.14.1			  2011-07-22		  Bio::Assembly::IO(3)
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