Sendu Bala
and 1 contributors


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


    use Bio::Assembly::IO;

    $in  = Bio::Assembly::IO->new(-file=>"<inputfilename",
    $out = Bio::Assembly::IO->new(-file=>">outputfilename",

    while ( my $seq = $in->next_seq() ) {


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


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.                  - General discussion  - About the mailing lists

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:


Robson Francisco de Souza





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


 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


 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


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


 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.