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

   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