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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:

	 https://github.com/bioperl/bioperl-live/issues

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

   format
	Title	: format
	Usage	: $format = $stream->format()
	Function: Get the assembly format
	Returns	: assembly format
	Args	: none

   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 v5.24.1			  2017-07-08		  Bio::Assembly::IO(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | CONTRIBUTORS | APPENDIX

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