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.

CPAN RT