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

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:

	 https://redmine.open-bio.org/projects/bioperl/

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

   next_contig
	Title	: next_contig
	Usage	: $contig = $stream->next_contig()
	Function: Reads the next contig or singlet from the stream and returns it.
	Returns : a Bio::Assembly::Contig or Bio::Contig::Assembly::Singlet
	Args	: none

   write_assembly
	 Title	 : write_assembly
	 Usage	 : $stream->write_assembly($assembly)
	 Function: Write the assembly object in desired format. This method calls
		   write_header(), write_contigs() and write_footer() internally.
	 Returns : 1 on success, 0 for error
	 Args	 : A Bio::Assembly::Scaffold object

   write_header
	 Title	 : write_header
	 Usage	 : $stream->write_header($assembly)
	 Function: Write the start of the assembly file. It can be called at any time,
		   not when starting to write the assembly file.
	 Returns : 1 on success, 0 for error
	 Args	 : A Bio::Assembly::Scaffold object or ... (check the specific format
		   driver for more details)

   write_contig
	 Title	 : write_contig
	 Usage	 : $stream->write_contig($contig)
	 Function: Write a contig object in the desired format.
	 Returns : 1 on success, 0 for error
	 Args	 : A Bio::Assembly::Contig object

   write_footer
	 Title	 : write_footer
	 Usage	 : $stream->write_footer($assembly)
	 Function: Write the start of the assembly file.
	 Returns : 1 on success, 0 for error
	 Args	 : A Bio::Assembly::Scaffold object or ... (check the specific format
		   driver for more details)

   _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
		  ace, phrap and tigr at the moment

   _sort
	   Title   : _sort
	   Usage   : @sorted_values = $ass_io->_sort(@values)
	   Function: Sort a list of values naturally if Sort::Naturally is installed
		     (nicer), lexically otherwise (not as nice, but safe)
	   Returns : array of sorted values
	   Args    : array of values to sort

perl v5.14.2							    2012-03-02						    Bio::Assembly::IO(3pm)